diff --git a/DESCRIPTION b/DESCRIPTION
index 485e1e17..8ceefd73 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: Racmacs
 Type: Package
 Title: R Antigenic Cartography Macros
-Version: 1.1.30
+Version: 1.1.35
 Date: 2022-02-23
 Author: Sam Wilks
 Maintainer: Sam Wilks <sw463@cam.ac.uk>
@@ -24,7 +24,8 @@ Imports:
     ellipsis,
     MASS,
     lifecycle,
-    igraph
+    igraph,
+    brotli
 LazyData: TRUE
 Suggests: 
     testthat,
diff --git a/NAMESPACE b/NAMESPACE
index 6a349331..2c3548b5 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -9,6 +9,7 @@ export("agAnnotations<-")
 export("agAspect<-")
 export("agBaseCoords<-")
 export("agClades<-")
+export("agContinent<-")
 export("agCoords<-")
 export("agDates<-")
 export("agExtra<-")
@@ -16,20 +17,22 @@ export("agFill<-")
 export("agGroups<-")
 export("agIDs<-")
 export("agLabIDs<-")
+export("agLineage<-")
 export("agNames<-")
-export("agNamesAbbreviated<-")
-export("agNamesFull<-")
+export("agNucleotideSequences<-")
 export("agOpacity<-")
 export("agOutline<-")
 export("agOutlineWidth<-")
 export("agPassage<-")
 export("agReactivityAdjustments<-")
+export("agReassortant<-")
 export("agReference<-")
 export("agRotation<-")
 export("agSequences<-")
 export("agShape<-")
 export("agShown<-")
 export("agSize<-")
+export("agStrings<-")
 export("dilutionStepsize<-")
 export("fixedColBases<-")
 export("layerNames<-")
@@ -52,19 +55,22 @@ export("srFill<-")
 export("srGroups<-")
 export("srHomologousAgs<-")
 export("srIDs<-")
+export("srLineage<-")
 export("srNames<-")
-export("srNamesAbbreviated<-")
-export("srNamesFull<-")
+export("srNucleotideSequences<-")
 export("srOpacity<-")
 export("srOutline<-")
 export("srOutlineWidth<-")
 export("srPassage<-")
+export("srReassortant<-")
 export("srReference<-")
 export("srRotation<-")
 export("srSequences<-")
 export("srShape<-")
 export("srShown<-")
 export("srSize<-")
+export("srSpecies<-")
+export("srStrings<-")
 export("titerTable<-")
 export(RacMerge.options)
 export(RacOptimizer.options)
@@ -82,6 +88,7 @@ export(agBootstrapBlob)
 export(agBootstrapCoords)
 export(agClades)
 export(agCohesion)
+export(agContinent)
 export(agCoords)
 export(agDates)
 export(agExtra)
@@ -90,13 +97,14 @@ export(agGroups)
 export(agIDs)
 export(agLabIDs)
 export(agLeverage)
+export(agLineage)
 export(agNames)
-export(agNamesAbbreviated)
-export(agNamesFull)
+export(agNucleotideSequences)
 export(agOutline)
 export(agOutlineWidth)
 export(agPassage)
 export(agReactivityAdjustments)
+export(agReassortant)
 export(agReference)
 export(agRotation)
 export(agSequences)
@@ -106,6 +114,7 @@ export(agSize)
 export(agStress)
 export(agStressBlobSize)
 export(agStressPerTiter)
+export(agStrings)
 export(agTriangulationBlobSize)
 export(allMapDimensions)
 export(allMapStresses)
@@ -163,6 +172,7 @@ export(numSera)
 export(numSeraGroups)
 export(optimizeAgReactivity)
 export(optimizeMap)
+export(optimizeSubsetAgsIndividually)
 export(orderAntigens)
 export(orderSera)
 export(plot_map_table_distance)
@@ -209,21 +219,24 @@ export(srGroups)
 export(srHomologousAgs)
 export(srIDs)
 export(srLeverage)
+export(srLineage)
 export(srNames)
-export(srNamesAbbreviated)
-export(srNamesFull)
+export(srNucleotideSequences)
 export(srOutline)
 export(srOutlineWidth)
 export(srPassage)
+export(srReassortant)
 export(srReference)
 export(srRotation)
 export(srSequences)
 export(srShape)
 export(srShown)
 export(srSize)
+export(srSpecies)
 export(srStress)
 export(srStressBlobSize)
 export(srStressPerTiter)
+export(srStrings)
 export(srTriangulationBlobSize)
 export(standardizeStrainNames)
 export(stressBlobs)
diff --git a/NEWS.md b/NEWS.md
index 1bdf611c..e9a186ae 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,4 @@
+
 # Racmacs 1.1.11
 * Added a `NEWS.md` file to track changes to the package.
 * Added test and correction for error where coordinates of under-constrained points were set to NaN for the first optimization run only, not all.
@@ -137,3 +138,27 @@
 # Racmacs 1.1.31
 * Added checks for disconnected groups of points and functions `mapCohesion()`, `agCohesion()`, `srCohesion()` to diagnose poorly connected groups of points
 * Add support for point transparency set either through `agOpacity()` and `srOpacity()` or appropriate hex code to the point fill or outline attribute e.g. `"#FF000099"`.
+
+# Racmacs 1.1.32
+* Disconnected maps now return an error rather than a warning
+* `agStressPerTiter()` and `srStressPerTiter()` now return a matrix with columns corresponding to stress per titer when nd values are excluded and when they are included
+* Corrected error when coloring maps by stress or showing error lines with disconnected points
+* If a titer table has column or row names but not sera or antigen names provided, names will be taken from the row and column names when creating a map.
+* Add support for reading maps with brotli compression
+* `agSequences()` and `srSequences()` now works when the stored sequences have different lengths or are missing for some points
+* Correct error where maps with duplicate antigen or serum names would not optimize
+
+# Racmacs 1.1.33
+* Add some basic support for viewing 1D maps
+* Fix an issue viewing sequence data where sequence data is not present for all antigens / sera
+* Fix an error reoptimize merging maps with no optimizations
+* Add verbosity argument to `mergeMaps()`
+* Verbosity argument also suppresses optimization progress messages
+* Issue a warning if duplicate antigen or serum names are found when creating a map
+
+# Racmacs 1.1.34
+* Add support for getting and setting serum species with `srSpecies()`.
+* Redundant attributes `agNamesAbbreviated`, `agNamesFull`, `srNamesAbbreviated`, `srNamesFull` removed
+
+# Racmacs 1.1.35
+* Add antigen and sera attributes: `agLineage()`, `srLineage()`, `agReassortant()`, `srReassortant()`, `agStrings()`, `srStrings()`, `agContinent()`, `agNucleotideSequences()`, `srNucleotideSequences()` 
diff --git a/R/RcppExports.R b/R/RcppExports.R
index 2cd30ef1..b536a6cf 100644
--- a/R/RcppExports.R
+++ b/R/RcppExports.R
@@ -93,16 +93,24 @@ ac_ag_get_name <- function(ag) {
     .Call('_Racmacs_ac_ag_get_name', PACKAGE = 'Racmacs', ag)
 }
 
-ac_ag_get_name_full <- function(ag) {
-    .Call('_Racmacs_ac_ag_get_name_full', PACKAGE = 'Racmacs', ag)
+ac_ag_get_extra <- function(ag) {
+    .Call('_Racmacs_ac_ag_get_extra', PACKAGE = 'Racmacs', ag)
 }
 
-ac_ag_get_name_abbreviated <- function(ag) {
-    .Call('_Racmacs_ac_ag_get_name_abbreviated', PACKAGE = 'Racmacs', ag)
+ac_ag_get_lineage <- function(ag) {
+    .Call('_Racmacs_ac_ag_get_lineage', PACKAGE = 'Racmacs', ag)
 }
 
-ac_ag_get_extra <- function(ag) {
-    .Call('_Racmacs_ac_ag_get_extra', PACKAGE = 'Racmacs', ag)
+ac_ag_get_reassortant <- function(ag) {
+    .Call('_Racmacs_ac_ag_get_reassortant', PACKAGE = 'Racmacs', ag)
+}
+
+ac_ag_get_strings <- function(ag) {
+    .Call('_Racmacs_ac_ag_get_strings', PACKAGE = 'Racmacs', ag)
+}
+
+ac_ag_get_continent <- function(ag) {
+    .Call('_Racmacs_ac_ag_get_continent', PACKAGE = 'Racmacs', ag)
 }
 
 ac_ag_get_match_id <- function(ag) {
@@ -149,16 +157,24 @@ ac_ag_set_name <- function(ag, value) {
     .Call('_Racmacs_ac_ag_set_name', PACKAGE = 'Racmacs', ag, value)
 }
 
-ac_ag_set_name_full <- function(ag, value) {
-    .Call('_Racmacs_ac_ag_set_name_full', PACKAGE = 'Racmacs', ag, value)
+ac_ag_set_extra <- function(ag, value) {
+    .Call('_Racmacs_ac_ag_set_extra', PACKAGE = 'Racmacs', ag, value)
+}
+
+ac_ag_set_lineage <- function(ag, value) {
+    .Call('_Racmacs_ac_ag_set_lineage', PACKAGE = 'Racmacs', ag, value)
 }
 
-ac_ag_set_name_abbreviated <- function(ag, value) {
-    .Call('_Racmacs_ac_ag_set_name_abbreviated', PACKAGE = 'Racmacs', ag, value)
+ac_ag_set_reassortant <- function(ag, value) {
+    .Call('_Racmacs_ac_ag_set_reassortant', PACKAGE = 'Racmacs', ag, value)
 }
 
-ac_ag_set_extra <- function(ag, value) {
-    .Call('_Racmacs_ac_ag_set_extra', PACKAGE = 'Racmacs', ag, value)
+ac_ag_set_strings <- function(ag, value) {
+    .Call('_Racmacs_ac_ag_set_strings', PACKAGE = 'Racmacs', ag, value)
+}
+
+ac_ag_set_continent <- function(ag, value) {
+    .Call('_Racmacs_ac_ag_set_continent', PACKAGE = 'Racmacs', ag, value)
 }
 
 ac_ag_set_group <- function(ag, value) {
@@ -345,6 +361,10 @@ ac_sr_get_passage <- function(sr) {
     .Call('_Racmacs_ac_sr_get_passage', PACKAGE = 'Racmacs', sr)
 }
 
+ac_sr_get_species <- function(sr) {
+    .Call('_Racmacs_ac_sr_get_species', PACKAGE = 'Racmacs', sr)
+}
+
 ac_sr_get_clade <- function(sr) {
     .Call('_Racmacs_ac_sr_get_clade', PACKAGE = 'Racmacs', sr)
 }
@@ -357,16 +377,24 @@ ac_sr_get_name <- function(sr) {
     .Call('_Racmacs_ac_sr_get_name', PACKAGE = 'Racmacs', sr)
 }
 
-ac_sr_get_name_full <- function(sr) {
-    .Call('_Racmacs_ac_sr_get_name_full', PACKAGE = 'Racmacs', sr)
+ac_sr_get_extra <- function(sr) {
+    .Call('_Racmacs_ac_sr_get_extra', PACKAGE = 'Racmacs', sr)
 }
 
-ac_sr_get_name_abbreviated <- function(sr) {
-    .Call('_Racmacs_ac_sr_get_name_abbreviated', PACKAGE = 'Racmacs', sr)
+ac_sr_get_lineage <- function(sr) {
+    .Call('_Racmacs_ac_sr_get_lineage', PACKAGE = 'Racmacs', sr)
 }
 
-ac_sr_get_extra <- function(sr) {
-    .Call('_Racmacs_ac_sr_get_extra', PACKAGE = 'Racmacs', sr)
+ac_sr_get_reassortant <- function(sr) {
+    .Call('_Racmacs_ac_sr_get_reassortant', PACKAGE = 'Racmacs', sr)
+}
+
+ac_sr_get_strings <- function(sr) {
+    .Call('_Racmacs_ac_sr_get_strings', PACKAGE = 'Racmacs', sr)
+}
+
+ac_sr_get_continent <- function(sr) {
+    .Call('_Racmacs_ac_sr_get_continent', PACKAGE = 'Racmacs', sr)
 }
 
 ac_sr_get_match_id <- function(sr) {
@@ -401,6 +429,10 @@ ac_sr_set_passage <- function(sr, value) {
     .Call('_Racmacs_ac_sr_set_passage', PACKAGE = 'Racmacs', sr, value)
 }
 
+ac_sr_set_species <- function(sr, value) {
+    .Call('_Racmacs_ac_sr_set_species', PACKAGE = 'Racmacs', sr, value)
+}
+
 ac_sr_set_clade <- function(sr, value) {
     .Call('_Racmacs_ac_sr_set_clade', PACKAGE = 'Racmacs', sr, value)
 }
@@ -413,16 +445,24 @@ ac_sr_set_name <- function(sr, value) {
     .Call('_Racmacs_ac_sr_set_name', PACKAGE = 'Racmacs', sr, value)
 }
 
-ac_sr_set_name_full <- function(sr, value) {
-    .Call('_Racmacs_ac_sr_set_name_full', PACKAGE = 'Racmacs', sr, value)
+ac_sr_set_extra <- function(sr, value) {
+    .Call('_Racmacs_ac_sr_set_extra', PACKAGE = 'Racmacs', sr, value)
 }
 
-ac_sr_set_name_abbreviated <- function(sr, value) {
-    .Call('_Racmacs_ac_sr_set_name_abbreviated', PACKAGE = 'Racmacs', sr, value)
+ac_sr_set_lineage <- function(sr, value) {
+    .Call('_Racmacs_ac_sr_set_lineage', PACKAGE = 'Racmacs', sr, value)
 }
 
-ac_sr_set_extra <- function(sr, value) {
-    .Call('_Racmacs_ac_sr_set_extra', PACKAGE = 'Racmacs', sr, value)
+ac_sr_set_reassortant <- function(sr, value) {
+    .Call('_Racmacs_ac_sr_set_reassortant', PACKAGE = 'Racmacs', sr, value)
+}
+
+ac_sr_set_strings <- function(sr, value) {
+    .Call('_Racmacs_ac_sr_set_strings', PACKAGE = 'Racmacs', sr, value)
+}
+
+ac_sr_set_continent <- function(sr, value) {
+    .Call('_Racmacs_ac_sr_set_continent', PACKAGE = 'Racmacs', sr, value)
 }
 
 ac_sr_set_homologous_ags <- function(sr, value) {
@@ -469,8 +509,8 @@ ac_merge_tables <- function(maps, merge_options) {
     .Call('_Racmacs_ac_merge_tables', PACKAGE = 'Racmacs', maps, merge_options)
 }
 
-ac_merge_reoptimized <- function(maps, num_dims, num_optimizations, optimizer_options, merge_options) {
-    .Call('_Racmacs_ac_merge_reoptimized', PACKAGE = 'Racmacs', maps, num_dims, num_optimizations, optimizer_options, merge_options)
+ac_merge_reoptimized <- function(maps, num_dims, num_optimizations, min_col_basis, optimizer_options, merge_options) {
+    .Call('_Racmacs_ac_merge_reoptimized', PACKAGE = 'Racmacs', maps, num_dims, num_optimizations, min_col_basis, optimizer_options, merge_options)
 }
 
 ac_merge_frozen_overlay <- function(maps, merge_options) {
diff --git a/R/map_loadsave.R b/R/map_loadsave.R
index 58119e57..da6783ec 100644
--- a/R/map_loadsave.R
+++ b/R/map_loadsave.R
@@ -30,7 +30,17 @@ read.acmap <- function(
 
   # Read the data from the file
   jsondata <- paste(readLines(filename, warn = FALSE), collapse = "\n")
-  map <- json_to_acmap(jsondata)
+  map <- tryCatch(
+    json_to_acmap(jsondata),
+    error = function(e) {
+      tryCatch(
+        read_brotli(filename),
+        error = function(e) {
+          stop("File '", filename, "' could not be parsed", call. = FALSE)
+        }
+      )
+    }
+  )
 
   # Apply arguments
   if (!is.null(optimization_number)) {
@@ -48,6 +58,13 @@ read.acmap <- function(
 
 }
 
+# Function to read brotli compressed maps
+read_brotli <- function(filepath) {
+  bin_file <- readBin(filepath, "raw", file.info(filepath)$size)
+  bin_uncompressed <- brotli::brotli_decompress(bin_file)
+  json_to_acmap(rawToChar(bin_uncompressed))
+}
+
 
 #' Save acmap data to a file
 #'
diff --git a/R/map_merge.R b/R/map_merge.R
index 5b84d344..47508211 100644
--- a/R/map_merge.R
+++ b/R/map_merge.R
@@ -14,6 +14,7 @@
 #' @param merge_options Options to use when merging titers (see `RacMerge.options()`).
 #' @param optimizer_options For merging that generates new optimization runs, optimizer
 #'   settings (see `RacOptimizer.options()`).
+#' @param verbose Should progress messages be output?
 #'
 #' @details Maps can be merged in a number of ways depending upon the desired
 #'   result.
@@ -62,7 +63,8 @@ mergeMaps <- function(
   number_of_optimizations,
   minimum_column_basis = "none",
   optimizer_options = list(),
-  merge_options = list()
+  merge_options = list(),
+  verbose = TRUE
   ) {
 
   # Process input
@@ -93,6 +95,7 @@ mergeMaps <- function(
   # Set options for any relaxation or optimizations
   optimizer_options <- do.call(RacOptimizer.options, optimizer_options)
   merge_options <- do.call(RacMerge.options, merge_options)
+  if (!verbose) optimizer_options$report_progress <- FALSE
 
   # Set the dilution stepsize for merging
   merge_options$dilution_stepsize <- mean(vapply(maps, dilutionStepsize, numeric(1)))
@@ -113,6 +116,7 @@ mergeMaps <- function(
         maps = maps,
         num_dims = number_of_dimensions,
         num_optimizations = number_of_optimizations,
+        min_col_basis = minimum_column_basis,
         optimizer_options = optimizer_options,
         merge_options = merge_options
       )
diff --git a/R/map_new.R b/R/map_new.R
index ae44b532..d77985ff 100644
--- a/R/map_new.R
+++ b/R/map_new.R
@@ -10,6 +10,8 @@
 #' @param ag_coords Antigenic coordinates for an optimization run record
 #'   (optional)
 #' @param sr_coords Sera coordinates for an optimization run record (optional)
+#' @param check_duplicates Issue a warning if duplicate antigen or sera names
+#'   are found
 #' @param ... Further arguments passed to `addOptimization()`
 #'
 #' @return Returns the new acmap object
@@ -32,6 +34,7 @@ acmap <- function(
   titer_table = NULL,
   ag_coords = NULL,
   sr_coords = NULL,
+  check_duplicates = TRUE,
   ...
 ) {
 
@@ -60,8 +63,18 @@ acmap <- function(
   )
 
   # Populate the map
-  if (!is.null(ag_names))    agNames(map)    <- ag_names
-  if (!is.null(sr_names))    srNames(map)    <- sr_names
+  if (!is.null(ag_names)) {
+    agNames(map) <- ag_names
+  } else if (!is.null(rownames(titer_table))) {
+    agNames(map) <- rownames(titer_table)
+  }
+
+  if (!is.null(sr_names)) {
+    srNames(map) <- sr_names
+  } else if (!is.null(colnames(titer_table))) {
+    srNames(map) <- colnames(titer_table)
+  }
+
   if (!is.null(titer_table)) titerTable(map) <- titer_table
 
   if (!is.null(ag_coords) || !is.null(sr_coords)) {
@@ -77,6 +90,12 @@ acmap <- function(
     }
   }
 
+  # Check for duplicate names
+  if (check_duplicates) {
+    if (sum(duplicated(agNames(map))) > 0) warning("Map contains duplicate antigen names")
+    if (sum(duplicated(srNames(map))) > 0) warning("Map contains duplicate sera names")
+  }
+
   # Return the new map
   map
 
diff --git a/R/map_optimize.R b/R/map_optimize.R
index 514e62a9..f95d5e58 100644
--- a/R/map_optimize.R
+++ b/R/map_optimize.R
@@ -69,6 +69,7 @@ optimizeMap <- function(
 
   # Get optimizer options
   options <- do.call(RacOptimizer.options, options)
+  if (!verbose) options$report_progress <- FALSE
 
   # Perform the optimization runs
   tstart <- Sys.time()
@@ -90,7 +91,13 @@ optimizeMap <- function(
   if (sum(sr_underconstrained) > 0) warn_underconstrained("SERA", srNames(map)[sr_underconstrained], number_of_dimensions)
 
   # Check for unconnected sets of points
-  if (mapDisconnected(map)) warning(no_cohesion_warning(), call. = F)
+  if (!options$ignore_disconnected && mapDisconnected(map)) {
+    stop(singleline(
+    "Map contains disconnected points (points that are not connected through
+     any path of detectable titers so cannot be coordinated relative to each other).
+     To optimize anyway, rerun with 'options = list(ignore_disconnected = TRUE)'."
+    ), call. = F)
+  }
 
   map <- ac_optimize_map(
     map = map,
@@ -126,10 +133,12 @@ optimizeMap <- function(
   # Check procrustes of the top 2 runs to see if there is much difference between them
   if (check_convergence && numOptimizations(map) > 1) {
 
-    procrustes_dists <- c(
-      procrustesData(map, map, comparison_optimization_number = 2)$ag_dists,
-      procrustesData(map, map, comparison_optimization_number = 2)$sr_dists
-    )
+    pcmap <- map
+    agNames(pcmap) <- paste("AG", seq_len(numAntigens(pcmap)))
+    srNames(pcmap) <- paste("SR", seq_len(numSera(pcmap)))
+
+    procrustes_data <- procrustesData(pcmap, pcmap, comparison_optimization_number = 2)
+    procrustes_dists <- c(procrustes_data$ag_dists, procrustes_data$sr_dists)
 
     if (max(procrustes_dists, na.rm = T) > 0.5) {
       warning(sprintf(
@@ -228,6 +237,7 @@ make.acmap <- function(
 #' @param maxit The maximum number of iterations to use in the optimizer
 #' @param num_cores The number of cores to run in parallel
 #' @param report_progress Should progress be reported
+#' @param ignore_disconnected Should the check for disconnected points be skipped
 #' @param progress_bar_length Progress bar length when progress is reported
 #'
 #' @details For more details, for example on "dimensional annealing" see
@@ -246,11 +256,13 @@ RacOptimizer.options <- function(
   maxit = 1000,
   num_cores = parallel::detectCores(),
   report_progress = NULL,
+  ignore_disconnected = FALSE,
   progress_bar_length = options()$width
 ) {
 
   # Check input
   check.logical(dim_annealing)
+  check.logical(ignore_disconnected)
   check.string(method)
   check.numeric(maxit)
   check.numeric(num_cores)
@@ -269,6 +281,7 @@ RacOptimizer.options <- function(
     method = method,
     maxit = maxit,
     num_cores = num_cores,
+    ignore_disconnected = ignore_disconnected,
     report_progress = report_progress,
     progress_bar_length = progress_bar_length
   )
@@ -588,6 +601,76 @@ moveTrappedPoints <- function(
 }
 
 
+
+#' Optimize a subset of antigens individually
+#'
+#' You may have a large subset of antigens that distort the positions of
+#' reference antigens and antisera. It can be useful to make a map containing
+#' only reference antigens and antisera, and add each antigen in the subset to
+#' the reference map individually. The resulting reference maps containing one
+#' additional antigen are then aligned, and the positions of the additional
+#' antigen in their individual map are shown.
+#'
+#' A common use case might be if you want to introduce many tens, or even
+#' hundreds, of mutants into an existing map, without the geometric patterns in
+#' the mutant's titrations swamping those between the existing antigens and
+#' sera.
+#'
+#' @param map The acmap object
+#' @param subset A list of antigen names to optimize individually.
+#' @param ... Arguments passed to optimizeMap. number_of_dimensions and
+#'   number_of_optimizations are mandatory.
+#'
+#' @return List containing 'merge' and 'individual'. 'merge' is the reference
+#'   map with with the positions of antigens in the subset overlain.
+#'   'individual' is a list containing each of the individual maps.
+#' @family {map optimization functions}
+#' @export
+#'
+optimizeSubsetAgsIndividually <- function(map, subset, ...) {
+
+  # Map lacking any antigen in the subset
+  refMap <- optimizeMap(removeAntigens(map, subset), ...)
+
+  # For storing coordinates of antigens in the subset
+  subsetCoords <- matrix(nrow = length(subset), ncol = mapDimensions(map))
+
+  maps <- list()
+
+  for (i in 1:length(subset)) {
+    # Remove all antigens in subset, except the ith
+    subsetMap <- removeAntigens(map, subset[-i])
+
+    # Optimize and align to reference
+    subsetMap <- optimizeMap(subsetMap, ...)
+    subsetMap <- realignMap(subsetMap, target_map = refMap)
+    coords <- agCoords(subsetMap)
+
+    # Find coordinates of remaining antigen in subset
+    ag <- subset[i]  # Name of the antigen
+    pos <- match(ag, agNames(subsetMap))  # Position of the antigen
+    subsetCoords[i,] <- coords[pos,]
+
+    # Store map
+    maps[ag] <- list(subsetMap)
+  }
+
+  # Make an acmap object, stitching together ag coordinates from the reference
+  # map, and coordinates of antigens in the subset
+  merge = acmap(
+    ag_names = c(agNames(refMap), subset),
+    sr_names = srNames(map),
+    ag_coords = rbind(agCoords(refMap), subsetCoords),
+    sr_coords = srCoords(refMap),
+    titer_table = titerTable(map),
+  )
+  merge <- applyPlotspec(map = merge, source_map = map)
+
+  # Return the merge and the individual maps
+  list(merge = merge, individual = maps)
+
+}
+
 # Functions for fetching hemisphering information
 agHemisphering <- function(map, optimization_number = 1) {
   lapply(agDiagnostics(map, optimization_number), function(ag) ag$hemi)
@@ -629,15 +712,6 @@ warn_disconnected <- function(type, strains, number_of_dimensions) {
   )
 }
 
-# Warnings to use
-no_cohesion_warning <- function() {
-  singleline(
-    "Some sets of points are entirely disconnected from each other meaning that the
-    resulting map will consist of disconnected sets of points that are not coordinated
-    relative to each other."
-  )
-}
-
 # Calculate map connectivity
 mapConnectivityGraph <- function(map) {
 
diff --git a/R/map_props_points_antigens.R b/R/map_props_points_antigens.R
index a18abf06..eeb003ab 100644
--- a/R/map_props_points_antigens.R
+++ b/R/map_props_points_antigens.R
@@ -58,10 +58,12 @@ antigens_setter <- function(fn, type) {
 #'     "agDates", "agDates<-",
 #'     "agReference", "agReference<-",
 #'     "agNames", "agNames<-",
-#'     "agNamesFull", "agNamesFull<-",
-#'     "agNamesAbbreviated", "agNamesAbbreviated<-",
 #'     "agExtra", "agExtra<-",
-#'     "agPassage", "agPassage<-"
+#'     "agPassage", "agPassage<-",
+#'     "agLineage", "agLineage<-",
+#'     "agReassortant", "agReassortant<-",
+#'     "agStrings", "agStrings<-",
+#'     "agContinent", "agContinent<-"
 #'   ),
 #'   args    = c("map")
 #' )
@@ -70,10 +72,12 @@ agIDs               <- antigens_getter(ac_ag_get_id)
 agDates             <- antigens_getter(ac_ag_get_date)
 agReference         <- antigens_getter(ac_ag_get_reference)
 agNames             <- antigens_getter(ac_ag_get_name)
-agNamesFull         <- antigens_getter(ac_ag_get_name_full)
-agNamesAbbreviated  <- antigens_getter(ac_ag_get_name_abbreviated)
 agExtra             <- antigens_getter(ac_ag_get_extra)
 agPassage           <- antigens_getter(ac_ag_get_passage)
+agLineage           <- antigens_getter(ac_ag_get_lineage)
+agReassortant       <- antigens_getter(ac_ag_get_reassortant)
+agStrings           <- antigens_getter(ac_ag_get_strings)
+agContinent         <- antigens_getter(ac_ag_get_continent)
 agGroupValues       <- antigens_getter(ac_ag_get_group) # Not exported
 agMatchIDs          <- antigens_getter(ac_ag_get_match_id) # Not exported
 
@@ -81,10 +85,12 @@ agMatchIDs          <- antigens_getter(ac_ag_get_match_id) # Not exported
 `agDates<-`             <- antigens_setter(ac_ag_set_date, "character")
 `agReference<-`         <- antigens_setter(ac_ag_set_reference, "character")
 `agNames<-`             <- antigens_setter(ac_ag_set_name, "character")
-`agNamesFull<-`         <- antigens_setter(ac_ag_set_name_full, "character")
-`agNamesAbbreviated<-`  <- antigens_setter(ac_ag_set_name_abbreviated, "character")
 `agExtra<-`             <- antigens_setter(ac_ag_set_extra, "character")
 `agPassage<-`           <- antigens_setter(ac_ag_set_passage, "character")
+`agLineage<-`           <- antigens_setter(ac_ag_set_lineage, "character")
+`agReassortant<-`       <- antigens_setter(ac_ag_set_reassortant, "character")
+`agStrings<-`           <- antigens_setter(ac_ag_set_strings, "character")
+`agContinent<-`         <- antigens_setter(ac_ag_set_continent, "character")
 `agGroupValues<-`       <- antigens_setter(ac_ag_set_group, "numeric") # Not exported
 
 
@@ -134,6 +140,8 @@ agGroups <- function(map) {
 #' Getting and setting antigen sequence information
 #'
 #' @param map The acmap data object
+#' @param missing_value Character to use to fill in portions of the sequence matrix
+#'   where sequence data is missing.
 #' @param value A character matrix of sequences with rows equal to the number of
 #'   antigens
 #'
@@ -143,13 +151,13 @@ agGroups <- function(map) {
 
 #' @rdname agSequences
 #' @export
-agSequences <- function(map) {
+agSequences <- function(map, missing_value = ".") {
   check.acmap(map)
-  do.call(
-    rbind,
+  rbind_list_to_matrix(
     lapply(map$antigens, function(ag) {
       strsplit(ag$sequence, "")[[1]]
-    })
+    }),
+    missing_value
   )
 }
 
@@ -166,6 +174,35 @@ agSequences <- function(map) {
   map
 }
 
+#' @rdname agSequences
+#' @export
+agNucleotideSequences <- function(map, missing_value = ".") {
+  check.acmap(map)
+  rbind_list_to_matrix(
+    lapply(map$antigens, function(ag) {
+      strsplit(ag$nucleotidesequence, "")[[1]]
+    }),
+    missing_value
+  )
+}
+
+#' @rdname agSequences
+#' @export
+`agNucleotideSequences<-` <- function(map, value) {
+  check.acmap(map)
+  if (nrow(value) != numAntigens(map)) {
+    stop("Number of sequences does not match number of antigens")
+  }
+  for (x in seq_len(numAntigens(map))) {
+    map$antigens[[x]]$nucleotidesequence <- paste0(value[x, ], collapse = "")
+  }
+  map
+}
+
+
+
+
+
 
 #' Getting and setting point clade information
 #'
diff --git a/R/map_props_points_sera.R b/R/map_props_points_sera.R
index cb94af2e..102f90ce 100644
--- a/R/map_props_points_sera.R
+++ b/R/map_props_points_sera.R
@@ -56,10 +56,12 @@ sera_setter <- function(fn, type) {
 #'     "srDates", "srDates<-",
 #'     "srReference", "srReference<-",
 #'     "srNames", "srNames<-",
-#'     "srNamesFull", "srNamesFull<-",
-#'     "srNamesAbbreviated", "srNamesAbbreviated<-",
 #'     "srExtra", "srExtra<-",
-#'     "srPassage", "srPassage<-"
+#'     "srPassage", "srPassage<-",
+#'     "srLineage", "srLineage<-",
+#'     "srReassortant", "srReassortant<-",
+#'     "srStrings", "srStrings<-",
+#'     "srSpecies", "srSpecies<-"
 #'   ),
 #'   args    = c("map")
 #' )
@@ -68,10 +70,12 @@ srIDs               <- sera_getter(ac_sr_get_id)
 srDates             <- sera_getter(ac_sr_get_date)
 srReference         <- sera_getter(ac_sr_get_reference)
 srNames             <- sera_getter(ac_sr_get_name)
-srNamesFull         <- sera_getter(ac_sr_get_name_full)
-srNamesAbbreviated  <- sera_getter(ac_sr_get_name_abbreviated)
 srExtra             <- sera_getter(ac_sr_get_extra)
 srPassage           <- sera_getter(ac_sr_get_passage)
+srLineage           <- sera_getter(ac_sr_get_lineage)
+srReassortant       <- sera_getter(ac_sr_get_reassortant)
+srStrings           <- sera_getter(ac_sr_get_strings)
+srSpecies           <- sera_getter(ac_sr_get_species)
 srGroupValues       <- sera_getter(ac_sr_get_group) # Not exported
 srMatchIDs          <- sera_getter(ac_sr_get_match_id) # Not exported
 
@@ -79,10 +83,12 @@ srMatchIDs          <- sera_getter(ac_sr_get_match_id) # Not exported
 `srDates<-`             <- sera_setter(ac_sr_set_date, "character")
 `srReference<-`         <- sera_setter(ac_sr_set_reference, "character")
 `srNames<-`             <- sera_setter(ac_sr_set_name, "character")
-`srNamesFull<-`         <- sera_setter(ac_sr_set_name_full, "character")
-`srNamesAbbreviated<-`  <- sera_setter(ac_sr_set_name_abbreviated, "character")
 `srExtra<-`             <- sera_setter(ac_sr_set_extra, "character")
 `srPassage<-`           <- sera_setter(ac_sr_set_passage, "character")
+`srLineage<-`           <- sera_setter(ac_sr_set_lineage, "character")
+`srReassortant<-`       <- sera_setter(ac_sr_set_reassortant, "character")
+`srStrings<-`           <- sera_setter(ac_sr_set_strings, "character")
+`srSpecies<-`           <- sera_setter(ac_sr_set_species, "character")
 `srGroupValues<-`       <- sera_setter(ac_sr_set_group, "numeric")
 
 
@@ -163,6 +169,8 @@ srGroups <- function(map) {
 #' Getting and setting sera sequence information
 #'
 #' @param map The acmap data object
+#' @param missing_value Character to use to fill in portions of the sequence matrix
+#'   where sequence data is missing.
 #' @param value A character matrix of sequences with rows equal to the number of
 #'   sera
 #'
@@ -172,13 +180,13 @@ srGroups <- function(map) {
 
 #' @rdname srSequences
 #' @export
-srSequences <- function(map) {
+srSequences <- function(map, missing_value = ".") {
   check.acmap(map)
-  do.call(
-    rbind,
+  rbind_list_to_matrix(
     lapply(map$sera, function(sr) {
       strsplit(sr$sequence, "")[[1]]
-    })
+    }),
+    missing_value
   )
 }
 
@@ -194,3 +202,28 @@ srSequences <- function(map) {
   }
   map
 }
+
+#' @rdname srSequences
+#' @export
+srNucleotideSequences <- function(map, missing_value = ".") {
+  check.acmap(map)
+  rbind_list_to_matrix(
+    lapply(map$sera, function(sr) {
+      strsplit(sr$nucleotidesequence, "")[[1]]
+    }),
+    missing_value
+  )
+}
+
+#' @rdname srSequences
+#' @export
+`srNucleotideSequences<-` <- function(map, value) {
+  check.acmap(map)
+  if (nrow(value) != numSera(map)) {
+    stop("Number of sequences does not match number of sera")
+  }
+  for (x in seq_len(numSera(map))) {
+    map$sera[[x]]$nucleotidesequence <- paste0(value[x, ], collapse = "")
+  }
+  map
+}
diff --git a/R/map_stress.R b/R/map_stress.R
index 27433de3..73f4b268 100644
--- a/R/map_stress.R
+++ b/R/map_stress.R
@@ -282,8 +282,6 @@ recalculateStress <- function(
 #'   name (defaults to all antigens).
 #' @param sera Which sera to check stress for, specified by index or name
 #'   (defaults to all sera).
-#' @param exclude_nd Should non-detectable values (e.g. <10) be excluded when
-#'   calculating point stress?
 #'
 #' @seealso See `mapStress()` for getting the total map stress directly.
 #' @family {map diagnostic functions}
@@ -334,8 +332,7 @@ srStress <- function(
 srStressPerTiter <- function(
   map,
   sera                = TRUE,
-  optimization_number = 1,
-  exclude_nd          = FALSE
+  optimization_number = 1
 ) {
 
   # Convert to indices
@@ -348,12 +345,21 @@ srStressPerTiter <- function(
   )
 
   # Exclude nd values
-  if (exclude_nd) stress_table[titertypesTable(map) != 1] <- NA
+  stress_table_nd_excluded <- stress_table
+  stress_table_nd_excluded[titertypesTable(map) != 1] <- NA
 
   # Calculate the antigen stress per titer
   stresses <- colMeans(stress_table, na.rm = T)
   stresses[is.na(srCoords(map))[,1]] <- NA
-  stresses[sera]
+
+  stresses_nd_excluded <- colMeans(stress_table_nd_excluded, na.rm = T)
+  stresses_nd_excluded[is.na(srCoords(map))[,1]] <- NA
+
+  # Return a matrix
+  result <- cbind(stresses, stresses_nd_excluded)
+  colnames(result) <- c("nd_included", "nd_excluded")
+  rownames(result) <- srNames(map)
+  result[sera, , drop = F]
 
 }
 
@@ -363,8 +369,7 @@ srStressPerTiter <- function(
 agStressPerTiter <- function(
   map,
   antigens            = TRUE,
-  optimization_number = 1,
-  exclude_nd          = FALSE
+  optimization_number = 1
 ) {
 
   # Convert to indices
@@ -377,12 +382,21 @@ agStressPerTiter <- function(
   )
 
   # Exclude nd values
-  if (exclude_nd) stress_table[titertypesTable(map) != 1] <- NA
+  stress_table_nd_excluded <- stress_table
+  stress_table_nd_excluded[titertypesTable(map) != 1] <- NA
 
   # Calculate the antigen stress per titer
   stresses <- rowMeans(stress_table, na.rm = T)
   stresses[is.na(agCoords(map))[,1]] <- NA
-  stresses[antigens]
+
+  stresses_nd_excluded <- rowMeans(stress_table_nd_excluded, na.rm = T)
+  stresses_nd_excluded[is.na(agCoords(map))[,1]] <- NA
+
+  # Return a matrix
+  result <- cbind(stresses, stresses_nd_excluded)
+  colnames(result) <- c("nd_included", "nd_excluded")
+  rownames(result) <- agNames(map)
+  result[antigens, , drop = F]
 
 }
 
diff --git a/R/plot_diagnostics.R b/R/plot_diagnostics.R
index 029d63e4..e2c1efb6 100644
--- a/R/plot_diagnostics.R
+++ b/R/plot_diagnostics.R
@@ -220,20 +220,34 @@ plotly_sr_titers <- function(
 }
 
 
-agMeanResiduals <- function(map, exclude_nd = TRUE) {
+agMeanResiduals <- function(map) {
 
   residuals <- mapResiduals(map)
-  if (exclude_nd) residuals[titertypesTable(map) != 1] <- NA
-  rowMeans(residuals, na.rm = T)
+  residuals_nd_excluded <- residuals
+  residuals_nd_excluded[titertypesTable(map) != 1] <- NA
+  result <- cbind(
+    rowMeans(residuals, na.rm = T),
+    rowMeans(residuals_nd_excluded, na.rm = T)
+  )
+  rownames(result) <- agNames(map)
+  colnames(result) <- c("nd_included", "nd_excluded")
+  result
 
 }
 
 
-srMeanResiduals <- function(map, exclude_nd = TRUE) {
+srMeanResiduals <- function(map) {
 
   residuals <- mapResiduals(map)
-  if (exclude_nd) residuals[titertypesTable(map) != 1] <- NA
-  colMeans(residuals, na.rm = T)
+  residuals_nd_excluded <- residuals
+  residuals_nd_excluded[titertypesTable(map) != 1] <- NA
+  result <- cbind(
+    colMeans(residuals, na.rm = T),
+    colMeans(residuals_nd_excluded, na.rm = T)
+  )
+  rownames(result) <- srNames(map)
+  colnames(result) <- c("nd_included", "nd_excluded")
+  result
 
 }
 
@@ -241,13 +255,9 @@ srMeanResiduals <- function(map, exclude_nd = TRUE) {
 plot_agMeanResiduals <- function(map, exclude_nd = TRUE, .plot = TRUE) {
   hist_ggplot(
     names  = agNames(map),
-    values = agMeanResiduals(map, exclude_nd),
+    values = agMeanResiduals(map)[,ifelse(exclude_nd, "nd_excluded", "nd_included")],
     title  = "Antigen mean residual error",
-    subtitle = switch(
-      exclude_nd,
-      "TRUE"  = "(nd excluded)",
-      "FALSE" = "(nd excluded)"
-    ),
+    subtitle = ifelse(exclude_nd, "(nd excluded)", "(nd excluded)"),
     vline = 0,
     .plot = .plot
   )
@@ -257,13 +267,9 @@ plot_agMeanResiduals <- function(map, exclude_nd = TRUE, .plot = TRUE) {
 plot_srMeanResiduals <- function(map, exclude_nd = TRUE, .plot = TRUE) {
   hist_ggplot(
     names  = srNames(map),
-    values = srMeanResiduals(map, exclude_nd),
+    values = srMeanResiduals(map)[,ifelse(exclude_nd, "nd_excluded", "nd_included")],
     title  = "Serum mean residual error",
-    subtitle = switch(
-      exclude_nd,
-      "TRUE"  = "(nd excluded)",
-      "FALSE" = "(nd excluded)"
-    ),
+    subtitle = ifelse(exclude_nd, "(nd excluded)", "(nd excluded)"),
     vline = 0,
     .plot = .plot
   )
@@ -283,7 +289,7 @@ plot_agStressPerTiter <- function(
 
   hist_ggplot(
     names  = agNames(map),
-    values = agStressPerTiter(map, exclude_nd = exclude_nd),
+    values = agStressPerTiter(map)[,ifelse(exclude_nd, "nd_excluded", "nd_included")],
     title  = "Antigen stress per titer",
     subtitle = switch(
       exclude_nd,
@@ -309,7 +315,7 @@ plot_srStressPerTiter <- function(
 
   hist_ggplot(
     names  = srNames(map),
-    values = srStressPerTiter(map, exclude_nd = exclude_nd),
+    values = srStressPerTiter(map)[,ifelse(exclude_nd, "nd_excluded", "nd_included")],
     title  = "Serum stress per titer",
     subtitle = switch(
       exclude_nd,
diff --git a/R/utils_matrix_getters.R b/R/utils_matrix_getters.R
index 757cf464..9cf0c2c4 100644
--- a/R/utils_matrix_getters.R
+++ b/R/utils_matrix_getters.R
@@ -68,3 +68,12 @@ srGroupOutline <- function(map) {
   names(sr_group_outlines) <- sr_groups
   sr_group_outlines
 }
+
+rbind_list_to_matrix <- function(x, missing_value = ".") {
+  maxlen <- max(vapply(x, length, numeric(1)))
+  x <- lapply(x, function(xi) {
+    missing_length <- maxlen - length(xi)
+    c(xi, rep(missing_value, missing_length))
+  })
+  do.call(rbind, x)
+}
diff --git a/R/utils_type_checking.R b/R/utils_type_checking.R
index 6deaf137..f9bf9f80 100644
--- a/R/utils_type_checking.R
+++ b/R/utils_type_checking.R
@@ -27,6 +27,13 @@ check.numeric <- function(x) {
   x
 }
 
+check.integer <- function(x) {
+  if (length(x) > 1 || !is.wholenumber(x)) {
+    stop("Input must be a single integer", call. = FALSE)
+  }
+  x
+}
+
 check.numericmatrix <- function(x) {
   if (!is.matrix(x) || !is.numeric(x)) {
     stop("Input must be a numeric matrix", call. = FALSE)
diff --git a/inst/htmlwidgets/RacViewer/lib/functions/agsr.js b/inst/htmlwidgets/RacViewer/lib/functions/agsr.js
index d25fd1df..727df209 100644
--- a/inst/htmlwidgets/RacViewer/lib/functions/agsr.js
+++ b/inst/htmlwidgets/RacViewer/lib/functions/agsr.js
@@ -118,6 +118,7 @@ Racmacs.Point = class Point {
         this.coords_na = args.coords === null || isNaN(args.coords[0]) || args.coords[0] === null;
         if(this.coords_na){
             this.coords3 = [0,0,0];
+            this.shown = false;
         } else {
             this.coords3 = args.coords.slice();
             while(this.coords3.length < 3){ this.coords3.push(0) }
@@ -177,15 +178,17 @@ Racmacs.Point = class Point {
     // Show point information
     showInfo(){
         
-        this.infoDiv = document.createElement("div");
-        this.infoDiv.innerHTML = this.name;
+        if (this.shown) {
+            this.infoDiv = document.createElement("div");
+            this.infoDiv.innerHTML = this.name;
 
-        if(this.viewer.coloring == "stress"){
-            this.infoDiv.innerHTML += ", Stress : "+this.stress.toFixed(2);
-            this.infoDiv.innerHTML += ", Mean stress : "+this.meanstress.toFixed(2);
+            if(this.viewer.coloring == "stress"){
+                this.infoDiv.innerHTML += ", Stress : "+this.stressval.toFixed(2);
+                this.infoDiv.innerHTML += ", Mean stress : "+this.meanstress.toFixed(2);
+            }
+            
+            this.viewer.addHoverInfo(this.infoDiv);
         }
-        
-        this.viewer.addHoverInfo(this.infoDiv);
 
     }
 
@@ -293,9 +296,10 @@ Racmacs.Point = class Point {
         if(this.blob){
             this.removeBlob();
         }
-        
+
         if(isNaN(to[0]) || isNaN(to[1]) || isNaN(to[2])){
             this.coords_na = true;
+            this.shown = false;
             to[0] = 0;
             to[1] = 0;
             to[2] = 0;
@@ -454,7 +458,8 @@ Racmacs.Point = class Point {
                     this.fillopacity = 0;
                 } else {
                     // If color is not transparent
-                    this.element.setFillOpacity(this.opacity);
+                    if (this.fillopacity == 0) this.fillopacity = this.viewer.styleset.noselections.unhovered.unselected.opacity;
+                    this.element.setFillOpacity(this.fillopacity);
                     this.element.setFillColor(col);
                 }
             }
@@ -528,17 +533,19 @@ Racmacs.Point = class Point {
     // Calculate the mean stress for this point
     calcMeanStress(){
 
+        if (this.coords_na) return(NaN);
         var num_detectable = 0;
         var stress = 0;
         for(var i=0; i<this.partners.length; i++){
             if(this.titerTo(this.partners[i]).charAt(0) != "<"
                && this.titerTo(this.partners[i]).charAt(0) != "*"
-               && this.titerTo(this.partners[i]).charAt(0) != "."){
+               && this.titerTo(this.partners[i]).charAt(0) != "."
+               && !this.partners[i].coords_na){
                 num_detectable++;
                 stress += this.stressTo(this.partners[i]);
             }
         }
-        this.stress = stress;
+        this.stressval = stress;
         this.meanstress = stress / num_detectable;
         return(this.meanstress);
 
diff --git a/inst/htmlwidgets/RacViewer/lib/functions/data.js b/inst/htmlwidgets/RacViewer/lib/functions/data.js
index 0c8ce368..34aee6b5 100644
--- a/inst/htmlwidgets/RacViewer/lib/functions/data.js
+++ b/inst/htmlwidgets/RacViewer/lib/functions/data.js
@@ -437,28 +437,48 @@ Racmacs.Data = class Data {
     agCoords(i){ return(this.ptCoords(i)); }
     srCoords(i){ return(this.ptCoords(i + this.numAntigens())); }
 
-    agSequences(i){
-        if(this.data.c.a[0].A) {
-            if(i === undefined) return(this.data.c.a.map( p => p.A.split("") ));
-            else                return(this.data.c.a[i].A.split(""));
-        } else if(this.data.c.x && this.data.c.x.a && this.data.c.x.a[0].q){
-            if(i === undefined) return(this.data.c.x.a.map( p => p.q.split("") ));
-            else                return(this.data.c.x.a[i].q.split(""));
-        } else {
-            return(null);
-        }
+    agSequences(){
+
+        let seqs = this.data.c.a.map((p, i) => {
+            if (p.A) {
+                return(p.A.split(""));
+            } else if (this.data.c.x && this.data.c.x.a && this.data.c.x.a[i].q) {
+                return(this.data.c.x.a[i].q.split(""));
+            } else {
+                return([]);
+            }
+        });
+        let maxlen = Math.max(...seqs.map(s => s.length));
+        seqs = seqs.map(s => {
+            while(s.length < maxlen) {
+                s.push(".");
+            }
+            return(s);
+        });
+        return(seqs);
+
     }
 
-    srSequences(i){
-        if(this.data.c.s[0].A) {
-            if(i === undefined) return(this.data.c.s.map( p => p.A.split("") ));
-            else                return(this.data.c.s[i].A.split(""));
-        } else if(this.data.c.x && this.data.c.x.s && this.data.c.x.s[0].q){
-            if(i === undefined) return(this.data.c.x.s.map( p => p.q.split("") ));
-            else                return(this.data.c.x.s[i].q.split(""));
-        } else {
-            return(null);
-        }
+    srSequences(){
+        
+        let seqs = this.data.c.s.map((p, i) => {
+            if (p.A) {
+                return(p.A.split(""));
+            } else if (this.data.c.x && this.data.c.x.s && this.data.c.x.s[i].q) {
+                return(this.data.c.x.s[i].q.split(""));
+            } else {
+                return([]);
+            }
+        });
+        let maxlen = Math.max(...seqs.map(s => s.length));
+        seqs = seqs.map(s => {
+            while(s.length < maxlen) {
+                s.push(".");
+            }
+            return(s);
+        });
+        return(seqs);
+
     }
 
     colbases(i=null){
diff --git a/inst/htmlwidgets/RacViewer/lib/functions/dimensions.js b/inst/htmlwidgets/RacViewer/lib/functions/dimensions.js
index f962ba13..408049c5 100644
--- a/inst/htmlwidgets/RacViewer/lib/functions/dimensions.js
+++ b/inst/htmlwidgets/RacViewer/lib/functions/dimensions.js
@@ -10,7 +10,7 @@ Racmacs.Viewer.prototype.setPlotDims = function(plotdims){
     );
     // this.scene.plotPoints.scale.set(1,1,1);
 
-    if(plotdims.dimensions == 2){
+    if(plotdims.dimensions <= 2){
 
         // Rebind navigation
         this.mouseMove = this.panScene;
@@ -84,7 +84,7 @@ Racmacs.Viewer.prototype.setDims = function(
     if (mapdims.zlim) this.mapdims.lims[2] = mapdims.zlim;
 
     // Work out map lims and aspect
-    if(this.mapdims.dimensions == 2) {
+    if(this.mapdims.dimensions <= 2) {
 
         // Set map limits
         this.mapdims.lims[2] = [-1, 1];
diff --git a/inst/htmlwidgets/RacViewer/lib/functions/graphics.js b/inst/htmlwidgets/RacViewer/lib/functions/graphics.js
index eaf4b5a7..7e5281a4 100644
--- a/inst/htmlwidgets/RacViewer/lib/functions/graphics.js
+++ b/inst/htmlwidgets/RacViewer/lib/functions/graphics.js
@@ -57,8 +57,10 @@ Racmacs.Viewer.prototype.colorPointsByStress = function(){
 
         for(var i=0; i<points.length; i++){
             var stress = points[i].calcMeanStress();
-            if(stress > max_stress || i==0){ max_stress = stress }
-            if(stress < min_stress || i==0){ min_stress = stress }
+            if (points[i].shown) {
+                if(stress > max_stress || max_stress === undefined){ max_stress = stress }
+                if(stress < min_stress || min_stress === undefined){ min_stress = stress }
+            }
         }
 
         for(var i=0; i<points.length; i++){
diff --git a/inst/htmlwidgets/RacViewer/lib/functions/grid.js b/inst/htmlwidgets/RacViewer/lib/functions/grid.js
index 1475b84d..68b2bd34 100644
--- a/inst/htmlwidgets/RacViewer/lib/functions/grid.js
+++ b/inst/htmlwidgets/RacViewer/lib/functions/grid.js
@@ -129,7 +129,7 @@ Racmacs.Grid.generate = function(args){
     bbox.max[2] = max_val;
 
     // Set variables based on number of dimensions
-	if(dimensions == 2){
+	if(dimensions <= 2){
 		
 		var num_grids = 1;
 
diff --git a/inst/htmlwidgets/RacViewer/lib/functions/points.js b/inst/htmlwidgets/RacViewer/lib/functions/points.js
index a53e95c5..422cbde3 100644
--- a/inst/htmlwidgets/RacViewer/lib/functions/points.js
+++ b/inst/htmlwidgets/RacViewer/lib/functions/points.js
@@ -52,7 +52,7 @@ Racmacs.Viewer.prototype.addAgSrPoints = function(){
     this.scene.empty();
 
     // For 2D maps
-    if(this.mapdims.dimensions == 2){
+    if(this.mapdims.dimensions <= 2){
 
         // For highly performant graphics
         if(this.performance_mode){
@@ -107,7 +107,7 @@ Racmacs.Viewer.prototype.addAgSrPoints = function(){
                 size : size,
                 shape : shape,
                 visible : visible,
-                dimensions : this.mapdims.dimensions,
+                dimensions : 2,
                 properties : properties,
                 viewer : this.scene.viewer,
                 order : order
diff --git a/inst/htmlwidgets/RacViewer/lib/functions/projections.js b/inst/htmlwidgets/RacViewer/lib/functions/projections.js
index 601ee027..487d8636 100644
--- a/inst/htmlwidgets/RacViewer/lib/functions/projections.js
+++ b/inst/htmlwidgets/RacViewer/lib/functions/projections.js
@@ -140,14 +140,14 @@ Racmacs.Viewer.prototype.switchToProjection = function(num){
     // Move antigen point coordinates
     for(var i=0; i<this.antigens.length; i++){
         var coords = this.data.agCoords(i);
-        if(coords.length == 2){ coords.push(0) }
+        while(coords.length < 3){ coords.push(0) }
         this.antigens[i].setPosition([coords[0], coords[1], coords[2]]);
     }
 
     // Move sera point coordinates
     for(var i=0; i<this.sera.length; i++){
         var coords = this.data.srCoords(i);
-        if(coords.length == 2){ coords.push(0) }
+        while(coords.length < 3){ coords.push(0) }
         this.sera[i].setPosition([coords[0], coords[1], coords[2]]);
     }
 
diff --git a/inst/htmlwidgets/RacViewer/lib/functions/selections.js b/inst/htmlwidgets/RacViewer/lib/functions/selections.js
index 23b2a281..23980bfb 100644
--- a/inst/htmlwidgets/RacViewer/lib/functions/selections.js
+++ b/inst/htmlwidgets/RacViewer/lib/functions/selections.js
@@ -369,7 +369,11 @@ Racmacs.Point.prototype.updateDisplay = function(){
             this.setOpacity(styles.unhovered.highlighted.opacity);
         } else {
             this.restoreOutlineColor();
-            this.restoreOpacity();
+            if (this.viewer.points_selected) {
+                this.setOpacity(styles.unhovered.unselected.opacity);
+            } else {
+                this.restoreOpacity();
+            }
         }
     }
 
diff --git a/inst/htmlwidgets/RacViewer/lib/functions/sequences.js b/inst/htmlwidgets/RacViewer/lib/functions/sequences.js
index 1bfd5bd8..fa0a189a 100644
--- a/inst/htmlwidgets/RacViewer/lib/functions/sequences.js
+++ b/inst/htmlwidgets/RacViewer/lib/functions/sequences.js
@@ -357,7 +357,7 @@ Racmacs.SequenceTable = class SequenceTable {
 					} else {
 					    var unique_seq = [];
 						sequences.map( s => { 
-							if(unique_seq.indexOf(s[i]) === -1){
+							if(s[i] != "." && unique_seq.indexOf(s[i]) === -1){
 								unique_seq.push(s[i]);
 							}
 						});
@@ -495,6 +495,7 @@ Racmacs.Viewer.prototype.colorPointsBySequence = function(pos){
 
     // Make missing aas grey
     aa_cols[unique_aas.indexOf("-")] = new THREE.Color("#cccccc");
+    aa_cols[unique_aas.indexOf(".")] = new THREE.Color("#cccccc");
 
     // Color points by aa
     aas.map((aa, i) => { 
diff --git a/inst/htmlwidgets/RacViewer/lib/functions/utils.js b/inst/htmlwidgets/RacViewer/lib/functions/utils.js
index edacc1b2..376b9378 100644
--- a/inst/htmlwidgets/RacViewer/lib/functions/utils.js
+++ b/inst/htmlwidgets/RacViewer/lib/functions/utils.js
@@ -183,7 +183,11 @@ Racmacs.utils.transformCoords = function(
 
 	if(coords[0] === null) return(coords);
 
-    if(coords.length == 2){
+    if(coords.length == 1){
+
+    	return(coords[0]*transformation[0]);
+
+    } else if(coords.length == 2){
     	
  		if(transformation.length == 4){
 	    	// Standard 2D transform
@@ -200,7 +204,7 @@ Racmacs.utils.transformCoords = function(
 	    	]);
 	    }
 
-    } else {
+    } else if(coords.length == 3) {
 
     	if(transformation.length == 9){
 	    	// Standard 3D transform
@@ -218,6 +222,10 @@ Racmacs.utils.transformCoords = function(
 	        ]);
 	    }
 
+    } else {
+
+    	throw("Cannot view more than 3 dimensions.");
+
     }
 
 }
@@ -229,8 +237,12 @@ Racmacs.utils.translateCoords = function(
 ){
 
 	if(coords[0] === null) return(coords);
-	
-    if(coords.length == 2){
+
+    if(coords.length == 1){
+
+    	return(coords[0]+translation[0]);
+
+    } else if(coords.length == 2){
     	
     	if(translation.length == 2){
 	    	// Standard 2D translation
@@ -247,7 +259,7 @@ Racmacs.utils.translateCoords = function(
 	        ]);
     	}
 
-    } else {
+    } else if(coords.length == 3) {
 
     	if(translation.length == 3){
 	    	// Standard 3D translation
@@ -265,6 +277,10 @@ Racmacs.utils.translateCoords = function(
 	        ]);
 	    }
 
+    } else {
+
+    	throw("Cannot view more than 3 dimensions.");
+    	
     }
 
 }
diff --git a/inst/htmlwidgets/RacViewer/lib/r3js/lib/functions/element_lines.js b/inst/htmlwidgets/RacViewer/lib/r3js/lib/functions/element_lines.js
index 4d27cd96..bcadffc8 100644
--- a/inst/htmlwidgets/RacViewer/lib/r3js/lib/functions/element_lines.js
+++ b/inst/htmlwidgets/RacViewer/lib/r3js/lib/functions/element_lines.js
@@ -49,7 +49,7 @@ R3JS.element.Line = class Line extends R3JS.element.base {
       } else {
         
         if(args.lwd > 0){
-          if(args.dimensions == 2){
+          if(args.dimensions <= 2){
             var geo = R3JS.Geometries.line2d({
               from: args.from,
               to: args.to,
diff --git a/man/RacOptimizer.options.Rd b/man/RacOptimizer.options.Rd
index 56e959cf..243d6aa5 100644
--- a/man/RacOptimizer.options.Rd
+++ b/man/RacOptimizer.options.Rd
@@ -10,6 +10,7 @@ RacOptimizer.options(
   maxit = 1000,
   num_cores = parallel::detectCores(),
   report_progress = NULL,
+  ignore_disconnected = FALSE,
   progress_bar_length = options()$width
 )
 }
@@ -24,6 +25,8 @@ RacOptimizer.options(
 
 \item{report_progress}{Should progress be reported}
 
+\item{ignore_disconnected}{Should the check for disconnected points be skipped}
+
 \item{progress_bar_length}{Progress bar length when progress is reported}
 }
 \value{
@@ -44,6 +47,7 @@ Other {map optimization functions}:
 \code{\link{make.acmap}()},
 \code{\link{moveTrappedPoints}()},
 \code{\link{optimizeMap}()},
+\code{\link{optimizeSubsetAgsIndividually}()},
 \code{\link{randomizeCoords}()},
 \code{\link{relaxMapOneStep}()},
 \code{\link{relaxMap}()}
diff --git a/man/acmap.Rd b/man/acmap.Rd
index d1e37300..004c5bb8 100644
--- a/man/acmap.Rd
+++ b/man/acmap.Rd
@@ -10,6 +10,7 @@ acmap(
   titer_table = NULL,
   ag_coords = NULL,
   sr_coords = NULL,
+  check_duplicates = TRUE,
   ...
 )
 }
@@ -25,6 +26,9 @@ acmap(
 
 \item{sr_coords}{Sera coordinates for an optimization run record (optional)}
 
+\item{check_duplicates}{Issue a warning if duplicate antigen or sera names
+are found}
+
 \item{...}{Further arguments passed to \code{addOptimization()}}
 }
 \value{
diff --git a/man/agAttributes.Rd b/man/agAttributes.Rd
index 4c957c57..6556f2b3 100644
--- a/man/agAttributes.Rd
+++ b/man/agAttributes.Rd
@@ -10,14 +10,18 @@
 \alias{agReference<-}
 \alias{agNames}
 \alias{agNames<-}
-\alias{agNamesFull}
-\alias{agNamesFull<-}
-\alias{agNamesAbbreviated}
-\alias{agNamesAbbreviated<-}
 \alias{agExtra}
 \alias{agExtra<-}
 \alias{agPassage}
 \alias{agPassage<-}
+\alias{agLineage}
+\alias{agLineage<-}
+\alias{agReassortant}
+\alias{agReassortant<-}
+\alias{agStrings}
+\alias{agStrings<-}
+\alias{agContinent}
+\alias{agContinent<-}
 \title{Getting and setting antigen attributes}
 \usage{
 agIDs(map)
@@ -28,14 +32,18 @@ agReference(map)
 agReference(map) <- value
 agNames(map)
 agNames(map) <- value
-agNamesFull(map)
-agNamesFull(map) <- value
-agNamesAbbreviated(map)
-agNamesAbbreviated(map) <- value
 agExtra(map)
 agExtra(map) <- value
 agPassage(map)
 agPassage(map) <- value
+agLineage(map)
+agLineage(map) <- value
+agReassortant(map)
+agReassortant(map) <- value
+agStrings(map)
+agStrings(map) <- value
+agContinent(map)
+agContinent(map) <- value
 }
 \arguments{
 \item{map}{The acmap data object}
diff --git a/man/agSequences.Rd b/man/agSequences.Rd
index 8fc1723b..b373b000 100644
--- a/man/agSequences.Rd
+++ b/man/agSequences.Rd
@@ -3,15 +3,24 @@
 \name{agSequences}
 \alias{agSequences}
 \alias{agSequences<-}
+\alias{agNucleotideSequences}
+\alias{agNucleotideSequences<-}
 \title{Getting and setting antigen sequence information}
 \usage{
-agSequences(map)
+agSequences(map, missing_value = ".")
 
 agSequences(map) <- value
+
+agNucleotideSequences(map, missing_value = ".")
+
+agNucleotideSequences(map) <- value
 }
 \arguments{
 \item{map}{The acmap data object}
 
+\item{missing_value}{Character to use to fill in portions of the sequence matrix
+where sequence data is missing.}
+
 \item{value}{A character matrix of sequences with rows equal to the number of
 antigens}
 }
diff --git a/man/make.acmap.Rd b/man/make.acmap.Rd
index e8be5b7f..30911e39 100644
--- a/man/make.acmap.Rd
+++ b/man/make.acmap.Rd
@@ -61,6 +61,7 @@ Other {map optimization functions}:
 \code{\link{RacOptimizer.options}()},
 \code{\link{moveTrappedPoints}()},
 \code{\link{optimizeMap}()},
+\code{\link{optimizeSubsetAgsIndividually}()},
 \code{\link{randomizeCoords}()},
 \code{\link{relaxMapOneStep}()},
 \code{\link{relaxMap}()}
diff --git a/man/mergeMaps.Rd b/man/mergeMaps.Rd
index 92e9114f..1dfae2c9 100644
--- a/man/mergeMaps.Rd
+++ b/man/mergeMaps.Rd
@@ -11,7 +11,8 @@ mergeMaps(
   number_of_optimizations,
   minimum_column_basis = "none",
   optimizer_options = list(),
-  merge_options = list()
+  merge_options = list(),
+  verbose = TRUE
 )
 }
 \arguments{
@@ -32,6 +33,8 @@ the minimum column basis to use.}
 settings (see \code{RacOptimizer.options()}).}
 
 \item{merge_options}{Options to use when merging titers (see \code{RacMerge.options()}).}
+
+\item{verbose}{Should progress messages be output?}
 }
 \value{
 Returns the merged map object
diff --git a/man/moveTrappedPoints.Rd b/man/moveTrappedPoints.Rd
index eaed8884..de9d1d3a 100644
--- a/man/moveTrappedPoints.Rd
+++ b/man/moveTrappedPoints.Rd
@@ -46,6 +46,7 @@ Other {map optimization functions}:
 \code{\link{RacOptimizer.options}()},
 \code{\link{make.acmap}()},
 \code{\link{optimizeMap}()},
+\code{\link{optimizeSubsetAgsIndividually}()},
 \code{\link{randomizeCoords}()},
 \code{\link{relaxMapOneStep}()},
 \code{\link{relaxMap}()}
diff --git a/man/optimizeMap.Rd b/man/optimizeMap.Rd
index 1dfdf63c..8d6862cb 100644
--- a/man/optimizeMap.Rd
+++ b/man/optimizeMap.Rd
@@ -75,6 +75,7 @@ Other {map optimization functions}:
 \code{\link{RacOptimizer.options}()},
 \code{\link{make.acmap}()},
 \code{\link{moveTrappedPoints}()},
+\code{\link{optimizeSubsetAgsIndividually}()},
 \code{\link{randomizeCoords}()},
 \code{\link{relaxMapOneStep}()},
 \code{\link{relaxMap}()}
diff --git a/man/optimizeSubsetAgsIndividually.Rd b/man/optimizeSubsetAgsIndividually.Rd
new file mode 100644
index 00000000..f267e828
--- /dev/null
+++ b/man/optimizeSubsetAgsIndividually.Rd
@@ -0,0 +1,46 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/map_optimize.R
+\name{optimizeSubsetAgsIndividually}
+\alias{optimizeSubsetAgsIndividually}
+\title{Optimize a subset of antigens individually}
+\usage{
+optimizeSubsetAgsIndividually(map, subset, ...)
+}
+\arguments{
+\item{map}{The acmap object}
+
+\item{subset}{A list of antigen names to optimize individually.}
+
+\item{...}{Arguments passed to optimizeMap. number_of_dimensions and
+number_of_optimizations are mandatory.}
+}
+\value{
+List containing 'merge' and 'individual'. 'merge' is the reference
+map with with the positions of antigens in the subset overlain.
+'individual' is a list containing each of the individual maps.
+}
+\description{
+You may have a large subset of antigens that distort the positions of
+reference antigens and antisera. It can be useful to make a map containing
+only reference antigens and antisera, and add each antigen in the subset to
+the reference map individually. The resulting reference maps containing one
+additional antigen are then aligned, and the positions of the additional
+antigen in their individual map are shown.
+}
+\details{
+A common use case might be if you want to introduce many tens, or even
+hundreds, of mutants into an existing map, without the geometric patterns in
+the mutant's titrations swamping those between the existing antigens and
+sera.
+}
+\seealso{
+Other {map optimization functions}: 
+\code{\link{RacOptimizer.options}()},
+\code{\link{make.acmap}()},
+\code{\link{moveTrappedPoints}()},
+\code{\link{optimizeMap}()},
+\code{\link{randomizeCoords}()},
+\code{\link{relaxMapOneStep}()},
+\code{\link{relaxMap}()}
+}
+\concept{{map optimization functions}}
diff --git a/man/pointStress.Rd b/man/pointStress.Rd
index 993fae14..0a293147 100644
--- a/man/pointStress.Rd
+++ b/man/pointStress.Rd
@@ -12,14 +12,9 @@ agStress(map, antigens = TRUE, optimization_number = 1)
 
 srStress(map, sera = TRUE, optimization_number = 1)
 
-srStressPerTiter(map, sera = TRUE, optimization_number = 1, exclude_nd = FALSE)
+srStressPerTiter(map, sera = TRUE, optimization_number = 1)
 
-agStressPerTiter(
-  map,
-  antigens = TRUE,
-  optimization_number = 1,
-  exclude_nd = FALSE
-)
+agStressPerTiter(map, antigens = TRUE, optimization_number = 1)
 }
 \arguments{
 \item{map}{The acmap data object}
@@ -31,9 +26,6 @@ name (defaults to all antigens).}
 
 \item{sera}{Which sera to check stress for, specified by index or name
 (defaults to all sera).}
-
-\item{exclude_nd}{Should non-detectable values (e.g. <10) be excluded when
-calculating point stress?}
 }
 \description{
 Functions to get stress associated with individual points in a map.
diff --git a/man/randomizeCoords.Rd b/man/randomizeCoords.Rd
index c3515f82..14ed187d 100644
--- a/man/randomizeCoords.Rd
+++ b/man/randomizeCoords.Rd
@@ -29,6 +29,7 @@ Other {map optimization functions}:
 \code{\link{make.acmap}()},
 \code{\link{moveTrappedPoints}()},
 \code{\link{optimizeMap}()},
+\code{\link{optimizeSubsetAgsIndividually}()},
 \code{\link{relaxMapOneStep}()},
 \code{\link{relaxMap}()}
 }
diff --git a/man/relaxMap.Rd b/man/relaxMap.Rd
index 7fbf6b31..6ac8c1cd 100644
--- a/man/relaxMap.Rd
+++ b/man/relaxMap.Rd
@@ -42,6 +42,7 @@ Other {map optimization functions}:
 \code{\link{make.acmap}()},
 \code{\link{moveTrappedPoints}()},
 \code{\link{optimizeMap}()},
+\code{\link{optimizeSubsetAgsIndividually}()},
 \code{\link{randomizeCoords}()},
 \code{\link{relaxMapOneStep}()}
 }
diff --git a/man/relaxMapOneStep.Rd b/man/relaxMapOneStep.Rd
index 23f2782f..83de691b 100644
--- a/man/relaxMapOneStep.Rd
+++ b/man/relaxMapOneStep.Rd
@@ -35,6 +35,7 @@ Other {map optimization functions}:
 \code{\link{make.acmap}()},
 \code{\link{moveTrappedPoints}()},
 \code{\link{optimizeMap}()},
+\code{\link{optimizeSubsetAgsIndividually}()},
 \code{\link{randomizeCoords}()},
 \code{\link{relaxMap}()}
 }
diff --git a/man/srAttributes.Rd b/man/srAttributes.Rd
index bcc5e1cd..e5cfca15 100644
--- a/man/srAttributes.Rd
+++ b/man/srAttributes.Rd
@@ -10,14 +10,18 @@
 \alias{srReference<-}
 \alias{srNames}
 \alias{srNames<-}
-\alias{srNamesFull}
-\alias{srNamesFull<-}
-\alias{srNamesAbbreviated}
-\alias{srNamesAbbreviated<-}
 \alias{srExtra}
 \alias{srExtra<-}
 \alias{srPassage}
 \alias{srPassage<-}
+\alias{srLineage}
+\alias{srLineage<-}
+\alias{srReassortant}
+\alias{srReassortant<-}
+\alias{srStrings}
+\alias{srStrings<-}
+\alias{srSpecies}
+\alias{srSpecies<-}
 \title{Getting and setting sera attributes}
 \usage{
 srIDs(map)
@@ -28,14 +32,18 @@ srReference(map)
 srReference(map) <- value
 srNames(map)
 srNames(map) <- value
-srNamesFull(map)
-srNamesFull(map) <- value
-srNamesAbbreviated(map)
-srNamesAbbreviated(map) <- value
 srExtra(map)
 srExtra(map) <- value
 srPassage(map)
 srPassage(map) <- value
+srLineage(map)
+srLineage(map) <- value
+srReassortant(map)
+srReassortant(map) <- value
+srStrings(map)
+srStrings(map) <- value
+srSpecies(map)
+srSpecies(map) <- value
 }
 \arguments{
 \item{map}{The acmap data object}
diff --git a/man/srSequences.Rd b/man/srSequences.Rd
index 925ea5e4..5b3633c4 100644
--- a/man/srSequences.Rd
+++ b/man/srSequences.Rd
@@ -3,15 +3,24 @@
 \name{srSequences}
 \alias{srSequences}
 \alias{srSequences<-}
+\alias{srNucleotideSequences}
+\alias{srNucleotideSequences<-}
 \title{Getting and setting sera sequence information}
 \usage{
-srSequences(map)
+srSequences(map, missing_value = ".")
 
 srSequences(map) <- value
+
+srNucleotideSequences(map, missing_value = ".")
+
+srNucleotideSequences(map) <- value
 }
 \arguments{
 \item{map}{The acmap data object}
 
+\item{missing_value}{Character to use to fill in portions of the sequence matrix
+where sequence data is missing.}
+
 \item{value}{A character matrix of sequences with rows equal to the number of
 sera}
 }
diff --git a/src/Racmacs_types.h b/src/Racmacs_types.h
index 2baaade0..60649717 100644
--- a/src/Racmacs_types.h
+++ b/src/Racmacs_types.h
@@ -168,6 +168,11 @@ SEXP wrap(const AcAntigen& ag){
       _["clade"] = ag.get_clade(),
       _["annotations"] = ag.get_annotations(),
       _["labids"] = ag.get_labids(),
+      _["lineage"] = ag.get_lineage(),
+      _["reassortant"] = ag.get_reassortant(),
+      _["strings"] = ag.get_strings(),
+      _["continent"] = ag.get_continent(),
+      _["nucleotidesequence"] = ag.get_nucleotidesequence(),
 
       // Plotspec
       _["plotspec"] = as<List>(wrap(ag.plotspec))
@@ -190,16 +195,20 @@ SEXP wrap(const AcSerum& sr){
       // Attributes
       _["name"] = sr.get_name(),
       _["extra"] = sr.get_extra(),
-      // _["name_abbreviated"] = sr.get_name_abbreviated(),
-      // _["name_full"] = sr.get_name_full(),
       _["id"] = sr.get_id(),
       _["date"] = sr.get_date(),
       _["group"] = sr.get_group(),
       _["homologous_ags"] = sr.get_homologous_ags(),
       _["sequence"] = sr.get_sequence(),
       _["passage"] = sr.get_passage(),
+      _["species"] = sr.get_species(),
       _["clade"] = sr.get_clade(),
       _["annotations"] = sr.get_annotations(),
+      _["lineage"] = sr.get_lineage(),
+      _["reassortant"] = sr.get_reassortant(),
+      _["strings"] = sr.get_strings(),
+      _["continent"] = sr.get_continent(),
+      _["nucleotidesequence"] = sr.get_nucleotidesequence(),
 
       // Plotspec
       _["plotspec"] = as<List>(wrap(sr.plotspec))
@@ -493,8 +502,6 @@ AcAntigen as(SEXP sxp){
   // Attributes
   if(list.containsElementNamed("name")) ag.set_name(list["name"]);
   if(list.containsElementNamed("extra")) ag.set_extra(list["extra"]);
-  // if(list.containsElementNamed("name_abbreviated")) ag.set_name_abbreviated(list["name_abbreviated"]);
-  // if(list.containsElementNamed("name_full")) ag.set_name_full(list["name_full"]);
   if(list.containsElementNamed("id")) ag.set_id(list["id"]);
   if(list.containsElementNamed("date")) ag.set_date(list["date"]);
   if(list.containsElementNamed("group")) ag.set_group(list["group"]);
@@ -503,6 +510,11 @@ AcAntigen as(SEXP sxp){
   if(list.containsElementNamed("clade")) ag.set_clade(list["clade"]);
   if(list.containsElementNamed("annotations")) ag.set_annotations(list["annotations"]);
   if(list.containsElementNamed("labids")) ag.set_labids(list["labids"]);
+  if(list.containsElementNamed("lineage")) ag.set_lineage(list["lineage"]);
+  if(list.containsElementNamed("reassortant")) ag.set_reassortant(list["reassortant"]);
+  if(list.containsElementNamed("strings")) ag.set_strings(list["strings"]);
+  if(list.containsElementNamed("continent")) ag.set_continent(list["continent"]);
+  if(list.containsElementNamed("nucleotidesequence")) ag.set_nucleotidesequence(list["nucleotidesequence"]);
 
   // Plotspec
   if(list.containsElementNamed("plotspec")) ag.plotspec = as<AcPlotspec>(list["plotspec"]);
@@ -530,8 +542,14 @@ AcSerum as(SEXP sxp){
   if(list.containsElementNamed("homologous_ags")) sr.set_homologous_ags(list["homologous_ags"]);
   if(list.containsElementNamed("sequence")) sr.set_sequence(list["sequence"]);
   if(list.containsElementNamed("passage")) sr.set_passage(list["passage"]);
+  if(list.containsElementNamed("species")) sr.set_species(list["species"]);
   if(list.containsElementNamed("clade")) sr.set_clade(list["clade"]);
   if(list.containsElementNamed("annotations")) sr.set_annotations(list["annotations"]);
+  if(list.containsElementNamed("lineage")) sr.set_lineage(list["lineage"]);
+  if(list.containsElementNamed("reassortant")) sr.set_reassortant(list["reassortant"]);
+  if(list.containsElementNamed("strings")) sr.set_strings(list["strings"]);
+  if(list.containsElementNamed("continent")) sr.set_continent(list["continent"]);
+  if(list.containsElementNamed("nucleotidesequence")) sr.set_nucleotidesequence(list["nucleotidesequence"]);
 
   // Plotspec
   if(list.containsElementNamed("plotspec")) sr.plotspec = as<AcPlotspec>(list["plotspec"]);
diff --git a/src/Racmacs_wrappers_antigens.cpp b/src/Racmacs_wrappers_antigens.cpp
index 446e4c82..3400f92e 100644
--- a/src/Racmacs_wrappers_antigens.cpp
+++ b/src/Racmacs_wrappers_antigens.cpp
@@ -31,11 +31,15 @@ std::vector<std::string> ac_ag_get_labids( const AcAntigen &ag ){ return ag.get_
 // [[Rcpp::export(rng = false)]]
 std::string ac_ag_get_name( const AcAntigen &ag ){ return ag.get_name(); }
 // [[Rcpp::export(rng = false)]]
-std::string ac_ag_get_name_full( const AcAntigen &ag ){ return ag.get_name_full(); }
+std::string ac_ag_get_extra( const AcAntigen &ag ){ return ag.get_extra(); }
 // [[Rcpp::export(rng = false)]]
-std::string ac_ag_get_name_abbreviated( const AcAntigen &ag ){ return ag.get_name_abbreviated(); }
+std::string ac_ag_get_lineage( const AcAntigen &ag ){ return ag.get_lineage(); }
 // [[Rcpp::export(rng = false)]]
-std::string ac_ag_get_extra( const AcAntigen &ag ){ return ag.get_extra(); }
+std::string ac_ag_get_reassortant( const AcAntigen &ag ){ return ag.get_reassortant(); }
+// [[Rcpp::export(rng = false)]]
+std::string ac_ag_get_strings( const AcAntigen &ag ){ return ag.get_strings(); }
+// [[Rcpp::export(rng = false)]]
+std::string ac_ag_get_continent( const AcAntigen &ag ){ return ag.get_continent(); }
 
 // [[Rcpp::export(rng = false)]]
 std::string ac_ag_get_match_id( const AcAntigen &ag ){ return ag.get_match_id(); }
@@ -64,11 +68,15 @@ AcAntigen ac_ag_set_labids( AcAntigen ag, std::vector<std::string> value ){ ag.s
 // [[Rcpp::export(rng = false)]]
 AcAntigen ac_ag_set_name( AcAntigen ag, std::string value ){ ag.set_name(value); return ag; }
 // [[Rcpp::export(rng = false)]]
-AcAntigen ac_ag_set_name_full( AcAntigen ag, std::string value ){  ag.set_name_full(value); return ag; }
+AcAntigen ac_ag_set_extra( AcAntigen ag, std::string value ){ ag.set_extra(value); return ag; }
 // [[Rcpp::export(rng = false)]]
-AcAntigen ac_ag_set_name_abbreviated( AcAntigen ag, std::string value ){ ag.set_name_abbreviated(value); return ag; }
+AcAntigen ac_ag_set_lineage( AcAntigen ag, std::string value ){ ag.set_lineage(value); return ag; }
 // [[Rcpp::export(rng = false)]]
-AcAntigen ac_ag_set_extra( AcAntigen ag, std::string value ){ ag.set_extra(value); return ag; }
+AcAntigen ac_ag_set_reassortant( AcAntigen ag, std::string value ){ ag.set_reassortant(value); return ag; }
+// [[Rcpp::export(rng = false)]]
+AcAntigen ac_ag_set_strings( AcAntigen ag, std::string value ){ ag.set_strings(value); return ag; }
+// [[Rcpp::export(rng = false)]]
+AcAntigen ac_ag_set_continent( AcAntigen ag, std::string value ){ ag.set_continent(value); return ag; }
 
 // [[Rcpp::export(rng = false)]]
 AcAntigen ac_ag_set_group( AcAntigen ag, int value ){ ag.set_group(value); return ag; }
diff --git a/src/Racmacs_wrappers_sera.cpp b/src/Racmacs_wrappers_sera.cpp
index 9f36b64f..97c6258c 100644
--- a/src/Racmacs_wrappers_sera.cpp
+++ b/src/Racmacs_wrappers_sera.cpp
@@ -23,17 +23,23 @@ bool ac_sr_get_reference( const AcSerum &sr ){ return sr.get_reference(); }
 // [[Rcpp::export(rng = false)]]
 std::string ac_sr_get_passage( const AcSerum &sr ){ return sr.get_passage(); }
 // [[Rcpp::export(rng = false)]]
+std::string ac_sr_get_species( const AcSerum &sr ){ return sr.get_species(); }
+// [[Rcpp::export(rng = false)]]
 std::vector<std::string> ac_sr_get_clade( const AcSerum &sr ){ return sr.get_clade(); }
 // [[Rcpp::export(rng = false)]]
 std::vector<std::string> ac_sr_get_annotations( const AcSerum &sr ){ return sr.get_annotations(); }
 // [[Rcpp::export(rng = false)]]
 std::string ac_sr_get_name( const AcSerum &sr ){ return sr.get_name(); }
 // [[Rcpp::export(rng = false)]]
-std::string ac_sr_get_name_full( const AcSerum &sr ){ return sr.get_name_full(); }
+std::string ac_sr_get_extra( const AcSerum &sr ){ return sr.get_extra(); }
 // [[Rcpp::export(rng = false)]]
-std::string ac_sr_get_name_abbreviated( const AcSerum &sr ){ return sr.get_name_abbreviated(); }
+std::string ac_sr_get_lineage( const AcSerum &sr ){ return sr.get_lineage(); }
 // [[Rcpp::export(rng = false)]]
-std::string ac_sr_get_extra( const AcSerum &sr ){ return sr.get_extra(); }
+std::string ac_sr_get_reassortant( const AcSerum &sr ){ return sr.get_reassortant(); }
+// [[Rcpp::export(rng = false)]]
+std::string ac_sr_get_strings( const AcSerum &sr ){ return sr.get_strings(); }
+// [[Rcpp::export(rng = false)]]
+std::string ac_sr_get_continent( const AcSerum &sr ){ return sr.get_continent(); }
 
 // [[Rcpp::export(rng = false)]]
 std::string ac_sr_get_match_id( const AcSerum &sr ){ return sr.get_match_id(); }
@@ -58,17 +64,24 @@ AcSerum ac_sr_set_reference( AcSerum sr, bool value ){  sr.set_reference(value);
 // [[Rcpp::export(rng = false)]]
 AcSerum ac_sr_set_passage( AcSerum sr, std::string value ){ sr.set_passage(value); return sr; }
 // [[Rcpp::export(rng = false)]]
+AcSerum ac_sr_set_species( AcSerum sr, std::string value ){ sr.set_species(value); return sr; }
+// [[Rcpp::export(rng = false)]]
 AcSerum ac_sr_set_clade( AcSerum sr, std::vector<std::string> value ){ sr.set_clade(value); return sr; }
 // [[Rcpp::export(rng = false)]]
 AcSerum ac_sr_set_annotations( AcSerum sr, std::vector<std::string> value ){ sr.set_annotations(value); return sr; }
 // [[Rcpp::export(rng = false)]]
 AcSerum ac_sr_set_name( AcSerum sr, std::string value ){ sr.set_name(value); return sr; }
 // [[Rcpp::export(rng = false)]]
-AcSerum ac_sr_set_name_full( AcSerum sr, std::string value ){  sr.set_name_full(value); return sr; }
+AcSerum ac_sr_set_extra( AcSerum sr, std::string value ){ sr.set_extra(value); return sr; }
 // [[Rcpp::export(rng = false)]]
-AcSerum ac_sr_set_name_abbreviated( AcSerum sr, std::string value ){ sr.set_name_abbreviated(value); return sr; }
+AcSerum ac_sr_set_lineage( AcSerum sr, std::string value ){ sr.set_lineage(value); return sr; }
 // [[Rcpp::export(rng = false)]]
-AcSerum ac_sr_set_extra( AcSerum sr, std::string value ){ sr.set_extra(value); return sr; }
+AcSerum ac_sr_set_reassortant( AcSerum sr, std::string value ){ sr.set_reassortant(value); return sr; }
+// [[Rcpp::export(rng = false)]]
+AcSerum ac_sr_set_strings( AcSerum sr, std::string value ){ sr.set_strings(value); return sr; }
+// [[Rcpp::export(rng = false)]]
+AcSerum ac_sr_set_continent( AcSerum sr, std::string value ){ sr.set_continent(value); return sr; }
+
 
 // [[Rcpp::export(rng = false)]]
 AcSerum ac_sr_set_homologous_ags( AcSerum sr, arma::uvec value ){ sr.set_homologous_ags(value); return sr; }
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
index 638bbcf4..67a8584b 100644
--- a/src/RcppExports.cpp
+++ b/src/RcppExports.cpp
@@ -286,33 +286,53 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
-// ac_ag_get_name_full
-std::string ac_ag_get_name_full(const AcAntigen& ag);
-RcppExport SEXP _Racmacs_ac_ag_get_name_full(SEXP agSEXP) {
+// ac_ag_get_extra
+std::string ac_ag_get_extra(const AcAntigen& ag);
+RcppExport SEXP _Racmacs_ac_ag_get_extra(SEXP agSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::traits::input_parameter< const AcAntigen& >::type ag(agSEXP);
-    rcpp_result_gen = Rcpp::wrap(ac_ag_get_name_full(ag));
+    rcpp_result_gen = Rcpp::wrap(ac_ag_get_extra(ag));
     return rcpp_result_gen;
 END_RCPP
 }
-// ac_ag_get_name_abbreviated
-std::string ac_ag_get_name_abbreviated(const AcAntigen& ag);
-RcppExport SEXP _Racmacs_ac_ag_get_name_abbreviated(SEXP agSEXP) {
+// ac_ag_get_lineage
+std::string ac_ag_get_lineage(const AcAntigen& ag);
+RcppExport SEXP _Racmacs_ac_ag_get_lineage(SEXP agSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::traits::input_parameter< const AcAntigen& >::type ag(agSEXP);
-    rcpp_result_gen = Rcpp::wrap(ac_ag_get_name_abbreviated(ag));
+    rcpp_result_gen = Rcpp::wrap(ac_ag_get_lineage(ag));
     return rcpp_result_gen;
 END_RCPP
 }
-// ac_ag_get_extra
-std::string ac_ag_get_extra(const AcAntigen& ag);
-RcppExport SEXP _Racmacs_ac_ag_get_extra(SEXP agSEXP) {
+// ac_ag_get_reassortant
+std::string ac_ag_get_reassortant(const AcAntigen& ag);
+RcppExport SEXP _Racmacs_ac_ag_get_reassortant(SEXP agSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::traits::input_parameter< const AcAntigen& >::type ag(agSEXP);
-    rcpp_result_gen = Rcpp::wrap(ac_ag_get_extra(ag));
+    rcpp_result_gen = Rcpp::wrap(ac_ag_get_reassortant(ag));
+    return rcpp_result_gen;
+END_RCPP
+}
+// ac_ag_get_strings
+std::string ac_ag_get_strings(const AcAntigen& ag);
+RcppExport SEXP _Racmacs_ac_ag_get_strings(SEXP agSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::traits::input_parameter< const AcAntigen& >::type ag(agSEXP);
+    rcpp_result_gen = Rcpp::wrap(ac_ag_get_strings(ag));
+    return rcpp_result_gen;
+END_RCPP
+}
+// ac_ag_get_continent
+std::string ac_ag_get_continent(const AcAntigen& ag);
+RcppExport SEXP _Racmacs_ac_ag_get_continent(SEXP agSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::traits::input_parameter< const AcAntigen& >::type ag(agSEXP);
+    rcpp_result_gen = Rcpp::wrap(ac_ag_get_continent(ag));
     return rcpp_result_gen;
 END_RCPP
 }
@@ -434,36 +454,58 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
-// ac_ag_set_name_full
-AcAntigen ac_ag_set_name_full(AcAntigen ag, std::string value);
-RcppExport SEXP _Racmacs_ac_ag_set_name_full(SEXP agSEXP, SEXP valueSEXP) {
+// ac_ag_set_extra
+AcAntigen ac_ag_set_extra(AcAntigen ag, std::string value);
+RcppExport SEXP _Racmacs_ac_ag_set_extra(SEXP agSEXP, SEXP valueSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::traits::input_parameter< AcAntigen >::type ag(agSEXP);
     Rcpp::traits::input_parameter< std::string >::type value(valueSEXP);
-    rcpp_result_gen = Rcpp::wrap(ac_ag_set_name_full(ag, value));
+    rcpp_result_gen = Rcpp::wrap(ac_ag_set_extra(ag, value));
     return rcpp_result_gen;
 END_RCPP
 }
-// ac_ag_set_name_abbreviated
-AcAntigen ac_ag_set_name_abbreviated(AcAntigen ag, std::string value);
-RcppExport SEXP _Racmacs_ac_ag_set_name_abbreviated(SEXP agSEXP, SEXP valueSEXP) {
+// ac_ag_set_lineage
+AcAntigen ac_ag_set_lineage(AcAntigen ag, std::string value);
+RcppExport SEXP _Racmacs_ac_ag_set_lineage(SEXP agSEXP, SEXP valueSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::traits::input_parameter< AcAntigen >::type ag(agSEXP);
     Rcpp::traits::input_parameter< std::string >::type value(valueSEXP);
-    rcpp_result_gen = Rcpp::wrap(ac_ag_set_name_abbreviated(ag, value));
+    rcpp_result_gen = Rcpp::wrap(ac_ag_set_lineage(ag, value));
     return rcpp_result_gen;
 END_RCPP
 }
-// ac_ag_set_extra
-AcAntigen ac_ag_set_extra(AcAntigen ag, std::string value);
-RcppExport SEXP _Racmacs_ac_ag_set_extra(SEXP agSEXP, SEXP valueSEXP) {
+// ac_ag_set_reassortant
+AcAntigen ac_ag_set_reassortant(AcAntigen ag, std::string value);
+RcppExport SEXP _Racmacs_ac_ag_set_reassortant(SEXP agSEXP, SEXP valueSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::traits::input_parameter< AcAntigen >::type ag(agSEXP);
     Rcpp::traits::input_parameter< std::string >::type value(valueSEXP);
-    rcpp_result_gen = Rcpp::wrap(ac_ag_set_extra(ag, value));
+    rcpp_result_gen = Rcpp::wrap(ac_ag_set_reassortant(ag, value));
+    return rcpp_result_gen;
+END_RCPP
+}
+// ac_ag_set_strings
+AcAntigen ac_ag_set_strings(AcAntigen ag, std::string value);
+RcppExport SEXP _Racmacs_ac_ag_set_strings(SEXP agSEXP, SEXP valueSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::traits::input_parameter< AcAntigen >::type ag(agSEXP);
+    Rcpp::traits::input_parameter< std::string >::type value(valueSEXP);
+    rcpp_result_gen = Rcpp::wrap(ac_ag_set_strings(ag, value));
+    return rcpp_result_gen;
+END_RCPP
+}
+// ac_ag_set_continent
+AcAntigen ac_ag_set_continent(AcAntigen ag, std::string value);
+RcppExport SEXP _Racmacs_ac_ag_set_continent(SEXP agSEXP, SEXP valueSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::traits::input_parameter< AcAntigen >::type ag(agSEXP);
+    Rcpp::traits::input_parameter< std::string >::type value(valueSEXP);
+    rcpp_result_gen = Rcpp::wrap(ac_ag_set_continent(ag, value));
     return rcpp_result_gen;
 END_RCPP
 }
@@ -951,6 +993,16 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
+// ac_sr_get_species
+std::string ac_sr_get_species(const AcSerum& sr);
+RcppExport SEXP _Racmacs_ac_sr_get_species(SEXP srSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::traits::input_parameter< const AcSerum& >::type sr(srSEXP);
+    rcpp_result_gen = Rcpp::wrap(ac_sr_get_species(sr));
+    return rcpp_result_gen;
+END_RCPP
+}
 // ac_sr_get_clade
 std::vector<std::string> ac_sr_get_clade(const AcSerum& sr);
 RcppExport SEXP _Racmacs_ac_sr_get_clade(SEXP srSEXP) {
@@ -981,33 +1033,53 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
-// ac_sr_get_name_full
-std::string ac_sr_get_name_full(const AcSerum& sr);
-RcppExport SEXP _Racmacs_ac_sr_get_name_full(SEXP srSEXP) {
+// ac_sr_get_extra
+std::string ac_sr_get_extra(const AcSerum& sr);
+RcppExport SEXP _Racmacs_ac_sr_get_extra(SEXP srSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::traits::input_parameter< const AcSerum& >::type sr(srSEXP);
+    rcpp_result_gen = Rcpp::wrap(ac_sr_get_extra(sr));
+    return rcpp_result_gen;
+END_RCPP
+}
+// ac_sr_get_lineage
+std::string ac_sr_get_lineage(const AcSerum& sr);
+RcppExport SEXP _Racmacs_ac_sr_get_lineage(SEXP srSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::traits::input_parameter< const AcSerum& >::type sr(srSEXP);
-    rcpp_result_gen = Rcpp::wrap(ac_sr_get_name_full(sr));
+    rcpp_result_gen = Rcpp::wrap(ac_sr_get_lineage(sr));
     return rcpp_result_gen;
 END_RCPP
 }
-// ac_sr_get_name_abbreviated
-std::string ac_sr_get_name_abbreviated(const AcSerum& sr);
-RcppExport SEXP _Racmacs_ac_sr_get_name_abbreviated(SEXP srSEXP) {
+// ac_sr_get_reassortant
+std::string ac_sr_get_reassortant(const AcSerum& sr);
+RcppExport SEXP _Racmacs_ac_sr_get_reassortant(SEXP srSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::traits::input_parameter< const AcSerum& >::type sr(srSEXP);
-    rcpp_result_gen = Rcpp::wrap(ac_sr_get_name_abbreviated(sr));
+    rcpp_result_gen = Rcpp::wrap(ac_sr_get_reassortant(sr));
     return rcpp_result_gen;
 END_RCPP
 }
-// ac_sr_get_extra
-std::string ac_sr_get_extra(const AcSerum& sr);
-RcppExport SEXP _Racmacs_ac_sr_get_extra(SEXP srSEXP) {
+// ac_sr_get_strings
+std::string ac_sr_get_strings(const AcSerum& sr);
+RcppExport SEXP _Racmacs_ac_sr_get_strings(SEXP srSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::traits::input_parameter< const AcSerum& >::type sr(srSEXP);
-    rcpp_result_gen = Rcpp::wrap(ac_sr_get_extra(sr));
+    rcpp_result_gen = Rcpp::wrap(ac_sr_get_strings(sr));
+    return rcpp_result_gen;
+END_RCPP
+}
+// ac_sr_get_continent
+std::string ac_sr_get_continent(const AcSerum& sr);
+RcppExport SEXP _Racmacs_ac_sr_get_continent(SEXP srSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::traits::input_parameter< const AcSerum& >::type sr(srSEXP);
+    rcpp_result_gen = Rcpp::wrap(ac_sr_get_continent(sr));
     return rcpp_result_gen;
 END_RCPP
 }
@@ -1095,6 +1167,17 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
+// ac_sr_set_species
+AcSerum ac_sr_set_species(AcSerum sr, std::string value);
+RcppExport SEXP _Racmacs_ac_sr_set_species(SEXP srSEXP, SEXP valueSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::traits::input_parameter< AcSerum >::type sr(srSEXP);
+    Rcpp::traits::input_parameter< std::string >::type value(valueSEXP);
+    rcpp_result_gen = Rcpp::wrap(ac_sr_set_species(sr, value));
+    return rcpp_result_gen;
+END_RCPP
+}
 // ac_sr_set_clade
 AcSerum ac_sr_set_clade(AcSerum sr, std::vector<std::string> value);
 RcppExport SEXP _Racmacs_ac_sr_set_clade(SEXP srSEXP, SEXP valueSEXP) {
@@ -1128,36 +1211,58 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
-// ac_sr_set_name_full
-AcSerum ac_sr_set_name_full(AcSerum sr, std::string value);
-RcppExport SEXP _Racmacs_ac_sr_set_name_full(SEXP srSEXP, SEXP valueSEXP) {
+// ac_sr_set_extra
+AcSerum ac_sr_set_extra(AcSerum sr, std::string value);
+RcppExport SEXP _Racmacs_ac_sr_set_extra(SEXP srSEXP, SEXP valueSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::traits::input_parameter< AcSerum >::type sr(srSEXP);
     Rcpp::traits::input_parameter< std::string >::type value(valueSEXP);
-    rcpp_result_gen = Rcpp::wrap(ac_sr_set_name_full(sr, value));
+    rcpp_result_gen = Rcpp::wrap(ac_sr_set_extra(sr, value));
     return rcpp_result_gen;
 END_RCPP
 }
-// ac_sr_set_name_abbreviated
-AcSerum ac_sr_set_name_abbreviated(AcSerum sr, std::string value);
-RcppExport SEXP _Racmacs_ac_sr_set_name_abbreviated(SEXP srSEXP, SEXP valueSEXP) {
+// ac_sr_set_lineage
+AcSerum ac_sr_set_lineage(AcSerum sr, std::string value);
+RcppExport SEXP _Racmacs_ac_sr_set_lineage(SEXP srSEXP, SEXP valueSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::traits::input_parameter< AcSerum >::type sr(srSEXP);
     Rcpp::traits::input_parameter< std::string >::type value(valueSEXP);
-    rcpp_result_gen = Rcpp::wrap(ac_sr_set_name_abbreviated(sr, value));
+    rcpp_result_gen = Rcpp::wrap(ac_sr_set_lineage(sr, value));
     return rcpp_result_gen;
 END_RCPP
 }
-// ac_sr_set_extra
-AcSerum ac_sr_set_extra(AcSerum sr, std::string value);
-RcppExport SEXP _Racmacs_ac_sr_set_extra(SEXP srSEXP, SEXP valueSEXP) {
+// ac_sr_set_reassortant
+AcSerum ac_sr_set_reassortant(AcSerum sr, std::string value);
+RcppExport SEXP _Racmacs_ac_sr_set_reassortant(SEXP srSEXP, SEXP valueSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::traits::input_parameter< AcSerum >::type sr(srSEXP);
     Rcpp::traits::input_parameter< std::string >::type value(valueSEXP);
-    rcpp_result_gen = Rcpp::wrap(ac_sr_set_extra(sr, value));
+    rcpp_result_gen = Rcpp::wrap(ac_sr_set_reassortant(sr, value));
+    return rcpp_result_gen;
+END_RCPP
+}
+// ac_sr_set_strings
+AcSerum ac_sr_set_strings(AcSerum sr, std::string value);
+RcppExport SEXP _Racmacs_ac_sr_set_strings(SEXP srSEXP, SEXP valueSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::traits::input_parameter< AcSerum >::type sr(srSEXP);
+    Rcpp::traits::input_parameter< std::string >::type value(valueSEXP);
+    rcpp_result_gen = Rcpp::wrap(ac_sr_set_strings(sr, value));
+    return rcpp_result_gen;
+END_RCPP
+}
+// ac_sr_set_continent
+AcSerum ac_sr_set_continent(AcSerum sr, std::string value);
+RcppExport SEXP _Racmacs_ac_sr_set_continent(SEXP srSEXP, SEXP valueSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::traits::input_parameter< AcSerum >::type sr(srSEXP);
+    Rcpp::traits::input_parameter< std::string >::type value(valueSEXP);
+    rcpp_result_gen = Rcpp::wrap(ac_sr_set_continent(sr, value));
     return rcpp_result_gen;
 END_RCPP
 }
@@ -1312,17 +1417,18 @@ BEGIN_RCPP
 END_RCPP
 }
 // ac_merge_reoptimized
-AcMap ac_merge_reoptimized(std::vector<AcMap> maps, int num_dims, int num_optimizations, AcOptimizerOptions optimizer_options, AcMergeOptions merge_options);
-RcppExport SEXP _Racmacs_ac_merge_reoptimized(SEXP mapsSEXP, SEXP num_dimsSEXP, SEXP num_optimizationsSEXP, SEXP optimizer_optionsSEXP, SEXP merge_optionsSEXP) {
+AcMap ac_merge_reoptimized(std::vector<AcMap> maps, int num_dims, int num_optimizations, std::string min_col_basis, AcOptimizerOptions optimizer_options, AcMergeOptions merge_options);
+RcppExport SEXP _Racmacs_ac_merge_reoptimized(SEXP mapsSEXP, SEXP num_dimsSEXP, SEXP num_optimizationsSEXP, SEXP min_col_basisSEXP, SEXP optimizer_optionsSEXP, SEXP merge_optionsSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::RNGScope rcpp_rngScope_gen;
     Rcpp::traits::input_parameter< std::vector<AcMap> >::type maps(mapsSEXP);
     Rcpp::traits::input_parameter< int >::type num_dims(num_dimsSEXP);
     Rcpp::traits::input_parameter< int >::type num_optimizations(num_optimizationsSEXP);
+    Rcpp::traits::input_parameter< std::string >::type min_col_basis(min_col_basisSEXP);
     Rcpp::traits::input_parameter< AcOptimizerOptions >::type optimizer_options(optimizer_optionsSEXP);
     Rcpp::traits::input_parameter< AcMergeOptions >::type merge_options(merge_optionsSEXP);
-    rcpp_result_gen = Rcpp::wrap(ac_merge_reoptimized(maps, num_dims, num_optimizations, optimizer_options, merge_options));
+    rcpp_result_gen = Rcpp::wrap(ac_merge_reoptimized(maps, num_dims, num_optimizations, min_col_basis, optimizer_options, merge_options));
     return rcpp_result_gen;
 END_RCPP
 }
@@ -1737,9 +1843,11 @@ static const R_CallMethodDef CallEntries[] = {
     {"_Racmacs_ac_ag_get_annotations", (DL_FUNC) &_Racmacs_ac_ag_get_annotations, 1},
     {"_Racmacs_ac_ag_get_labids", (DL_FUNC) &_Racmacs_ac_ag_get_labids, 1},
     {"_Racmacs_ac_ag_get_name", (DL_FUNC) &_Racmacs_ac_ag_get_name, 1},
-    {"_Racmacs_ac_ag_get_name_full", (DL_FUNC) &_Racmacs_ac_ag_get_name_full, 1},
-    {"_Racmacs_ac_ag_get_name_abbreviated", (DL_FUNC) &_Racmacs_ac_ag_get_name_abbreviated, 1},
     {"_Racmacs_ac_ag_get_extra", (DL_FUNC) &_Racmacs_ac_ag_get_extra, 1},
+    {"_Racmacs_ac_ag_get_lineage", (DL_FUNC) &_Racmacs_ac_ag_get_lineage, 1},
+    {"_Racmacs_ac_ag_get_reassortant", (DL_FUNC) &_Racmacs_ac_ag_get_reassortant, 1},
+    {"_Racmacs_ac_ag_get_strings", (DL_FUNC) &_Racmacs_ac_ag_get_strings, 1},
+    {"_Racmacs_ac_ag_get_continent", (DL_FUNC) &_Racmacs_ac_ag_get_continent, 1},
     {"_Racmacs_ac_ag_get_match_id", (DL_FUNC) &_Racmacs_ac_ag_get_match_id, 1},
     {"_Racmacs_ac_ag_get_group", (DL_FUNC) &_Racmacs_ac_ag_get_group, 1},
     {"_Racmacs_ac_ag_get_group_levels", (DL_FUNC) &_Racmacs_ac_ag_get_group_levels, 1},
@@ -1751,9 +1859,11 @@ static const R_CallMethodDef CallEntries[] = {
     {"_Racmacs_ac_ag_set_annotations", (DL_FUNC) &_Racmacs_ac_ag_set_annotations, 2},
     {"_Racmacs_ac_ag_set_labids", (DL_FUNC) &_Racmacs_ac_ag_set_labids, 2},
     {"_Racmacs_ac_ag_set_name", (DL_FUNC) &_Racmacs_ac_ag_set_name, 2},
-    {"_Racmacs_ac_ag_set_name_full", (DL_FUNC) &_Racmacs_ac_ag_set_name_full, 2},
-    {"_Racmacs_ac_ag_set_name_abbreviated", (DL_FUNC) &_Racmacs_ac_ag_set_name_abbreviated, 2},
     {"_Racmacs_ac_ag_set_extra", (DL_FUNC) &_Racmacs_ac_ag_set_extra, 2},
+    {"_Racmacs_ac_ag_set_lineage", (DL_FUNC) &_Racmacs_ac_ag_set_lineage, 2},
+    {"_Racmacs_ac_ag_set_reassortant", (DL_FUNC) &_Racmacs_ac_ag_set_reassortant, 2},
+    {"_Racmacs_ac_ag_set_strings", (DL_FUNC) &_Racmacs_ac_ag_set_strings, 2},
+    {"_Racmacs_ac_ag_set_continent", (DL_FUNC) &_Racmacs_ac_ag_set_continent, 2},
     {"_Racmacs_ac_ag_set_group", (DL_FUNC) &_Racmacs_ac_ag_set_group, 2},
     {"_Racmacs_ac_ag_set_group_levels", (DL_FUNC) &_Racmacs_ac_ag_set_group_levels, 2},
     {"_Racmacs_ac_opt_get_ag_base_coords", (DL_FUNC) &_Racmacs_ac_opt_get_ag_base_coords, 1},
@@ -1800,12 +1910,15 @@ static const R_CallMethodDef CallEntries[] = {
     {"_Racmacs_ac_sr_get_date", (DL_FUNC) &_Racmacs_ac_sr_get_date, 1},
     {"_Racmacs_ac_sr_get_reference", (DL_FUNC) &_Racmacs_ac_sr_get_reference, 1},
     {"_Racmacs_ac_sr_get_passage", (DL_FUNC) &_Racmacs_ac_sr_get_passage, 1},
+    {"_Racmacs_ac_sr_get_species", (DL_FUNC) &_Racmacs_ac_sr_get_species, 1},
     {"_Racmacs_ac_sr_get_clade", (DL_FUNC) &_Racmacs_ac_sr_get_clade, 1},
     {"_Racmacs_ac_sr_get_annotations", (DL_FUNC) &_Racmacs_ac_sr_get_annotations, 1},
     {"_Racmacs_ac_sr_get_name", (DL_FUNC) &_Racmacs_ac_sr_get_name, 1},
-    {"_Racmacs_ac_sr_get_name_full", (DL_FUNC) &_Racmacs_ac_sr_get_name_full, 1},
-    {"_Racmacs_ac_sr_get_name_abbreviated", (DL_FUNC) &_Racmacs_ac_sr_get_name_abbreviated, 1},
     {"_Racmacs_ac_sr_get_extra", (DL_FUNC) &_Racmacs_ac_sr_get_extra, 1},
+    {"_Racmacs_ac_sr_get_lineage", (DL_FUNC) &_Racmacs_ac_sr_get_lineage, 1},
+    {"_Racmacs_ac_sr_get_reassortant", (DL_FUNC) &_Racmacs_ac_sr_get_reassortant, 1},
+    {"_Racmacs_ac_sr_get_strings", (DL_FUNC) &_Racmacs_ac_sr_get_strings, 1},
+    {"_Racmacs_ac_sr_get_continent", (DL_FUNC) &_Racmacs_ac_sr_get_continent, 1},
     {"_Racmacs_ac_sr_get_match_id", (DL_FUNC) &_Racmacs_ac_sr_get_match_id, 1},
     {"_Racmacs_ac_sr_get_homologous_ags", (DL_FUNC) &_Racmacs_ac_sr_get_homologous_ags, 1},
     {"_Racmacs_ac_sr_get_group", (DL_FUNC) &_Racmacs_ac_sr_get_group, 1},
@@ -1814,12 +1927,15 @@ static const R_CallMethodDef CallEntries[] = {
     {"_Racmacs_ac_sr_set_date", (DL_FUNC) &_Racmacs_ac_sr_set_date, 2},
     {"_Racmacs_ac_sr_set_reference", (DL_FUNC) &_Racmacs_ac_sr_set_reference, 2},
     {"_Racmacs_ac_sr_set_passage", (DL_FUNC) &_Racmacs_ac_sr_set_passage, 2},
+    {"_Racmacs_ac_sr_set_species", (DL_FUNC) &_Racmacs_ac_sr_set_species, 2},
     {"_Racmacs_ac_sr_set_clade", (DL_FUNC) &_Racmacs_ac_sr_set_clade, 2},
     {"_Racmacs_ac_sr_set_annotations", (DL_FUNC) &_Racmacs_ac_sr_set_annotations, 2},
     {"_Racmacs_ac_sr_set_name", (DL_FUNC) &_Racmacs_ac_sr_set_name, 2},
-    {"_Racmacs_ac_sr_set_name_full", (DL_FUNC) &_Racmacs_ac_sr_set_name_full, 2},
-    {"_Racmacs_ac_sr_set_name_abbreviated", (DL_FUNC) &_Racmacs_ac_sr_set_name_abbreviated, 2},
     {"_Racmacs_ac_sr_set_extra", (DL_FUNC) &_Racmacs_ac_sr_set_extra, 2},
+    {"_Racmacs_ac_sr_set_lineage", (DL_FUNC) &_Racmacs_ac_sr_set_lineage, 2},
+    {"_Racmacs_ac_sr_set_reassortant", (DL_FUNC) &_Racmacs_ac_sr_set_reassortant, 2},
+    {"_Racmacs_ac_sr_set_strings", (DL_FUNC) &_Racmacs_ac_sr_set_strings, 2},
+    {"_Racmacs_ac_sr_set_continent", (DL_FUNC) &_Racmacs_ac_sr_set_continent, 2},
     {"_Racmacs_ac_sr_set_homologous_ags", (DL_FUNC) &_Racmacs_ac_sr_set_homologous_ags, 2},
     {"_Racmacs_ac_sr_set_group", (DL_FUNC) &_Racmacs_ac_sr_set_group, 2},
     {"_Racmacs_ac_sr_set_group_levels", (DL_FUNC) &_Racmacs_ac_sr_set_group_levels, 2},
@@ -1831,7 +1947,7 @@ static const R_CallMethodDef CallEntries[] = {
     {"_Racmacs_ac_merge_titers", (DL_FUNC) &_Racmacs_ac_merge_titers, 2},
     {"_Racmacs_ac_merge_titer_layers", (DL_FUNC) &_Racmacs_ac_merge_titer_layers, 2},
     {"_Racmacs_ac_merge_tables", (DL_FUNC) &_Racmacs_ac_merge_tables, 2},
-    {"_Racmacs_ac_merge_reoptimized", (DL_FUNC) &_Racmacs_ac_merge_reoptimized, 5},
+    {"_Racmacs_ac_merge_reoptimized", (DL_FUNC) &_Racmacs_ac_merge_reoptimized, 6},
     {"_Racmacs_ac_merge_frozen_overlay", (DL_FUNC) &_Racmacs_ac_merge_frozen_overlay, 2},
     {"_Racmacs_ac_merge_relaxed_overlay", (DL_FUNC) &_Racmacs_ac_merge_relaxed_overlay, 3},
     {"_Racmacs_ac_merge_frozen_merge", (DL_FUNC) &_Racmacs_ac_merge_frozen_merge, 3},
diff --git a/src/ac_merge.cpp b/src/ac_merge.cpp
index 4d05de95..f74aadc8 100644
--- a/src/ac_merge.cpp
+++ b/src/ac_merge.cpp
@@ -277,9 +277,9 @@ arma::vec merge_ag_reactivity_adjustments(
     for(arma::uword j=0; j<matches.n_elem; j++){
 
       double merged_ag_reactivity_adjustment = merged_ag_reactivity_adjustments( matches(j) );
-      double map_ag_reactivity_adjustment = maps[i].optimizations[0].get_ag_reactivity_adjustments(j);
+      double map_ag_reactivity_adjustment = maps[i].get_ag_reactivity_adjustments(j);
 
-      if(std::isfinite(merged_ag_reactivity_adjustment) && merged_ag_reactivity_adjustment != map_ag_reactivity_adjustment){
+      if(std::isfinite(merged_ag_reactivity_adjustment) && merged_ag_reactivity_adjustment != map_ag_reactivity_adjustment) {
         // Warn if different ag reactivity adjustments used
         Rcpp::Rcerr << "\nAntigen reactivity adjustments of merged maps do not match, they will be taken from the first map";
       } else {
@@ -423,6 +423,7 @@ AcMap ac_merge_reoptimized(
   std::vector<AcMap> maps,
   int num_dims,
   int num_optimizations,
+  std::string min_col_basis,
   AcOptimizerOptions optimizer_options,
   AcMergeOptions merge_options
 ){
@@ -430,10 +431,6 @@ AcMap ac_merge_reoptimized(
   // Merge the map tables
   AcMap merged_map = ac_merge_tables(maps, merge_options);
 
-  // Merge column bases
-  std::string min_col_basis = merge_min_column_basis( maps );
-  arma::vec fixed_col_bases = merge_fixed_column_bases( maps, merged_map.sera );
-
   // Merge antigen reactivity adjustments
   arma::vec ag_reactivity_adjustments = merge_ag_reactivity_adjustments( maps, merged_map.antigens );
 
@@ -442,7 +439,7 @@ AcMap ac_merge_reoptimized(
     num_dims,
     num_optimizations,
     min_col_basis,
-    fixed_col_bases,
+    arma::vec(merged_map.antigens.size(), arma::fill::value(arma::datum::nan)),
     ag_reactivity_adjustments,
     optimizer_options
   );
diff --git a/src/acmap_point.cpp b/src/acmap_point.cpp
index 44334895..0b7f4ab5 100644
--- a/src/acmap_point.cpp
+++ b/src/acmap_point.cpp
@@ -11,14 +11,18 @@ std::string AcPoint::get_extra() const { return extra; }
 std::string AcPoint::get_date() const { return date; }
 bool AcPoint::get_reference() const { return reference; }
 std::string AcPoint::get_passage() const { return passage; }
-std::string AcPoint::get_name_full() const { return name_full; }
-std::string AcPoint::get_name_abbreviated() const { return name_abbreviated; }
 std::string AcPoint::get_id() const { return id; }
+std::string AcPoint::get_species() const { return species; }
 int AcPoint::get_group() const { return group; }
 std::string AcPoint::get_sequence() const { return sequence; }
 std::vector<std::string> AcPoint::get_clade() const { return clade; }
 std::vector<std::string> AcPoint::get_annotations() const { return annotations; }
 std::vector<std::string> AcPoint::get_labids() const { return labids; }
+std::string AcPoint::get_lineage() const { return lineage; }
+std::string AcPoint::get_reassortant() const { return reassortant; }
+std::string AcPoint::get_strings() const { return strings; }
+std::string AcPoint::get_continent() const { return continent; }
+std::string AcPoint::get_nucleotidesequence() const { return nucleotidesequence; }
 
 void AcPoint::set_type( std::string value ){ type = value; }
 void AcPoint::set_name( std::string value ){ name = value; }
@@ -26,14 +30,18 @@ void AcPoint::set_extra( std::string value ){ extra = value; }
 void AcPoint::set_date( std::string value ){ date = value; }
 void AcPoint::set_reference( bool value ){ reference = value; }
 void AcPoint::set_passage( std::string value ){ passage = value; }
-void AcPoint::set_name_full( std::string value ){ name_full = value; }
-void AcPoint::set_name_abbreviated( std::string value ){ name_abbreviated = value; }
 void AcPoint::set_id( std::string value ){ id = value; }
+void AcPoint::set_species( std::string value ){ species = value; }
 void AcPoint::set_group( int value ){ group = value; }
 void AcPoint::set_sequence( std::string value ){ sequence = value; }
 void AcPoint::set_clade( std::vector<std::string> value ){ clade = value; }
 void AcPoint::set_annotations( std::vector<std::string> value ){ annotations = value; }
 void AcPoint::set_labids( std::vector<std::string> value ){ labids = value; }
+void AcPoint::set_lineage( std::string value ){ lineage = value; }
+void AcPoint::set_reassortant( std::string value ){ reassortant = value; }
+void AcPoint::set_strings( std::string value ){ strings = value; }
+void AcPoint::set_continent( std::string value ){ continent = value; }
+void AcPoint::set_nucleotidesequence( std::string value ){ nucleotidesequence = value; }
 
 // Get IDs for matching
 std::string AcPoint::get_match_id() const {
@@ -63,8 +71,20 @@ bool AcPoint::isdefault(std::string attribute) {
     return(id == "");
   } else if (attribute == "extra") {
     return(extra == "");
+  } else if (attribute == "species") {
+    return(species == "");
   } else if (attribute == "date") {
     return(date == "");
+  } else if (attribute == "lineage") {
+    return(lineage == "");
+  } else if (attribute == "reassortant") {
+    return(reassortant == "");
+  } else if (attribute == "strings") {
+    return(strings == "");
+  } else if (attribute == "continent") {
+    return(continent == "");
+  } else if (attribute == "nucleotidesequence") {
+    return(nucleotidesequence == "");
   } else {
     return(false);
   }
diff --git a/src/acmap_point.h b/src/acmap_point.h
index d8a80c18..03f59f49 100644
--- a/src/acmap_point.h
+++ b/src/acmap_point.h
@@ -17,15 +17,19 @@ class AcPoint {
     std::string extra;
     std::string date;
     bool reference = false;
-    std::string name_full;
-    std::string name_abbreviated;
     std::string id = "";
     int group = 0;
     std::string sequence;
     std::string passage;
+    std::string species;
     std::vector<std::string> clade;
     std::vector<std::string> annotations;
     std::vector<std::string> labids;
+    std::string lineage;
+    std::string reassortant;
+    std::string strings;
+    std::string continent;
+    std::string nucleotidesequence;
 
   public:
 
@@ -42,14 +46,18 @@ class AcPoint {
     std::string get_date() const;
     bool get_reference() const;
     std::string get_passage() const;
-    std::string get_name_full() const;
-    std::string get_name_abbreviated() const;
     std::string get_id() const;
+    std::string get_species() const;
     int get_group() const;
     std::string get_sequence() const;
     std::vector<std::string> get_clade() const;
     std::vector<std::string> get_annotations() const;
     std::vector<std::string> get_labids() const;
+    std::string get_lineage() const;
+    std::string get_reassortant() const;
+    std::string get_strings() const;
+    std::string get_continent() const;
+    std::string get_nucleotidesequence() const;
 
     void set_type( std::string value );
     void set_name( std::string value );
@@ -57,14 +65,18 @@ class AcPoint {
     void set_date( std::string value );
     void set_reference( bool value );
     void set_passage( std::string value );
-    void set_name_full( std::string value );
-    void set_name_abbreviated( std::string value );
     void set_id( std::string value );
+    void set_species( std::string value );
     void set_group( int value );
     void set_sequence( std::string value );
     void set_clade( std::vector<std::string> value );
     void set_annotations( std::vector<std::string> value );
     void set_labids( std::vector<std::string> value );
+    void set_lineage( std::string value );
+    void set_reassortant( std::string value );
+    void set_strings( std::string value );
+    void set_continent( std::string value );
+    void set_nucleotidesequence( std::string value );
 
     // Get IDs for matching
     std::string get_match_id() const;
diff --git a/src/json_read_to_acmap.cpp b/src/json_read_to_acmap.cpp
index ded0d0c3..465fa594 100644
--- a/src/json_read_to_acmap.cpp
+++ b/src/json_read_to_acmap.cpp
@@ -93,6 +93,11 @@ AcMap json_to_acmap(
     if(ag.HasMember("l")) map.antigens[i].set_labids( parse<std::vector<std::string>>(ag["l"]) );
     if(ag.HasMember("A")) map.antigens[i].set_sequence( ag["A"].GetString() );
     if(ag.HasMember("D")) map.antigens[i].set_date( ag["D"].GetString() );
+    if(ag.HasMember("L")) map.antigens[i].set_lineage( ag["L"].GetString() );
+    if(ag.HasMember("R")) map.antigens[i].set_reassortant( ag["R"].GetString() );
+    if(ag.HasMember("S")) map.antigens[i].set_strings( ag["S"].GetString() );
+    if(ag.HasMember("C")) map.antigens[i].set_continent( ag["C"].GetString() );
+    if(ag.HasMember("B")) map.antigens[i].set_nucleotidesequence( ag["B"].GetString() );
     // set_reference
     // set_name_full
     // set_name_abbreviated
@@ -112,7 +117,13 @@ AcMap json_to_acmap(
     if(sr.HasMember("A")) map.sera[i].set_sequence( sr["A"].GetString() );
     if(sr.HasMember("D")) map.sera[i].set_date( sr["D"].GetString() );
     if(sr.HasMember("I")) map.sera[i].set_id( sr["I"].GetString() );
+    if(sr.HasMember("s")) map.sera[i].set_species( sr["s"].GetString() );
     if(sr.HasMember("h")) map.sera[i].set_homologous_ags( parse<arma::uvec>(sr["h"]) );
+    if(sr.HasMember("L")) map.sera[i].set_lineage( sr["L"].GetString() );
+    if(sr.HasMember("R")) map.sera[i].set_reassortant( sr["R"].GetString() );
+    if(sr.HasMember("S")) map.sera[i].set_strings( sr["S"].GetString() );
+    if(sr.HasMember("C")) map.sera[i].set_continent( sr["C"].GetString() );
+    if(sr.HasMember("B")) map.sera[i].set_nucleotidesequence( sr["B"].GetString() );
     // set_reference
     // set_name_full
     // set_name_abbreviated
diff --git a/src/json_write_from_acmap.cpp b/src/json_write_from_acmap.cpp
index 84e7363e..b550d51a 100644
--- a/src/json_write_from_acmap.cpp
+++ b/src/json_write_from_acmap.cpp
@@ -52,12 +52,17 @@ std::string acmap_to_json(
     Value agval(kObjectType);
 
     agval.AddMember("N", jsonifya(ag.get_name(), allocator), allocator);
-    if (!ag.isdefault("passage"))     agval.AddMember("P", jsonifya(ag.get_passage(), allocator), allocator);
-    if (!ag.isdefault("clade"))       agval.AddMember("c", jsonifya(ag.get_clade(), allocator), allocator);
-    if (!ag.isdefault("annotations")) agval.AddMember("a", jsonifya(ag.get_annotations(), allocator), allocator);
-    if (!ag.isdefault("labids"))      agval.AddMember("l", jsonifya(ag.get_labids(), allocator), allocator);
-    if (!ag.isdefault("sequence"))    agval.AddMember("A", jsonifya(ag.get_sequence(), allocator), allocator);
-    if (!ag.isdefault("date"))        agval.AddMember("D", jsonifya(ag.get_date(), allocator), allocator);
+    if (!ag.isdefault("passage"))            agval.AddMember("P", jsonifya(ag.get_passage(), allocator), allocator);
+    if (!ag.isdefault("clade"))              agval.AddMember("c", jsonifya(ag.get_clade(), allocator), allocator);
+    if (!ag.isdefault("annotations"))        agval.AddMember("a", jsonifya(ag.get_annotations(), allocator), allocator);
+    if (!ag.isdefault("labids"))             agval.AddMember("l", jsonifya(ag.get_labids(), allocator), allocator);
+    if (!ag.isdefault("sequence"))           agval.AddMember("A", jsonifya(ag.get_sequence(), allocator), allocator);
+    if (!ag.isdefault("date"))               agval.AddMember("D", jsonifya(ag.get_date(), allocator), allocator);
+    if (!ag.isdefault("lineage"))            agval.AddMember("L", jsonifya(ag.get_lineage(), allocator), allocator);
+    if (!ag.isdefault("reassortant"))        agval.AddMember("R", jsonifya(ag.get_reassortant(), allocator), allocator);
+    if (!ag.isdefault("strings"))            agval.AddMember("S", jsonifya(ag.get_strings(), allocator), allocator);
+    if (!ag.isdefault("continent"))          agval.AddMember("C", jsonifya(ag.get_continent(), allocator), allocator);
+    if (!ag.isdefault("nucleotidesequence")) agval.AddMember("B", jsonifya(ag.get_nucleotidesequence(), allocator), allocator);
     // set_group_values
     // set_reference
     // set_name_full
@@ -75,13 +80,20 @@ std::string acmap_to_json(
     Value srval(kObjectType);
 
     srval.AddMember("N", jsonifya(sr.get_name(), allocator), allocator);
-    if (!sr.isdefault("passage"))           srval.AddMember("P", jsonifya(sr.get_passage(), allocator), allocator);
-    if (!sr.isdefault("clade"))             srval.AddMember("c", jsonifya(sr.get_clade(), allocator), allocator);
-    if (!sr.isdefault("annotations"))       srval.AddMember("a", jsonifya(sr.get_annotations(), allocator), allocator);
-    if (!sr.isdefault("sequence"))          srval.AddMember("A", jsonifya(sr.get_sequence(), allocator), allocator);
-    if (!sr.isdefault("date"))              srval.AddMember("D", jsonifya(sr.get_date(), allocator), allocator);
-    if (!sr.isdefault("id"))                srval.AddMember("I", jsonifya(sr.get_id(), allocator), allocator);
-    if (sr.get_homologous_ags().n_elem > 0) srval.AddMember("h", jsonifya(sr.get_homologous_ags(), allocator), allocator);
+    if (!sr.isdefault("passage"))            srval.AddMember("P", jsonifya(sr.get_passage(), allocator), allocator);
+    if (!sr.isdefault("clade"))              srval.AddMember("c", jsonifya(sr.get_clade(), allocator), allocator);
+    if (!sr.isdefault("annotations"))        srval.AddMember("a", jsonifya(sr.get_annotations(), allocator), allocator);
+    if (!sr.isdefault("sequence"))           srval.AddMember("A", jsonifya(sr.get_sequence(), allocator), allocator);
+    if (!sr.isdefault("date"))               srval.AddMember("D", jsonifya(sr.get_date(), allocator), allocator);
+    if (!sr.isdefault("id"))                 srval.AddMember("I", jsonifya(sr.get_id(), allocator), allocator);
+    if (!sr.isdefault("species"))           srval.AddMember("s", jsonifya(sr.get_species(), allocator), allocator);
+    if (sr.get_homologous_ags().n_elem > 0)  srval.AddMember("h", jsonifya(sr.get_homologous_ags(), allocator), allocator);
+    if (!sr.isdefault("lineage"))            srval.AddMember("L", jsonifya(sr.get_lineage(), allocator), allocator);
+    if (!sr.isdefault("reassortant"))        srval.AddMember("R", jsonifya(sr.get_reassortant(), allocator), allocator);
+    if (!sr.isdefault("strings"))            srval.AddMember("S", jsonifya(sr.get_strings(), allocator), allocator);
+    if (!sr.isdefault("continent"))          srval.AddMember("C", jsonifya(sr.get_continent(), allocator), allocator);
+    if (!sr.isdefault("nucleotidesequence")) srval.AddMember("B", jsonifya(sr.get_nucleotidesequence(), allocator), allocator);
+
     // set_group_values
     // set_reference
     // set_name_full
diff --git a/tests/testthat/test-diagnostics_stress.R b/tests/testthat/test-diagnostics_stress.R
index 6246ce67..e98384c6 100644
--- a/tests/testthat/test-diagnostics_stress.R
+++ b/tests/testthat/test-diagnostics_stress.R
@@ -28,8 +28,8 @@ test_that("point stress per titer", {
   ag_stress_per_titer <- agStressPerTiter(map)
   sr_stress_per_titer <- srStressPerTiter(map)
 
-  expect_equal(length(ag_stress_per_titer), numAntigens(map))
-  expect_equal(length(sr_stress_per_titer), numSera(map))
+  expect_equal(nrow(ag_stress_per_titer), numAntigens(map))
+  expect_equal(nrow(sr_stress_per_titer), numSera(map))
 
 })
 
@@ -81,7 +81,7 @@ test_that("Stress with NA coords", {
   map <- make.acmap(dat)
 
   expect_equal(
-    round(agStressPerTiter(map, exclude_nd = T)[4], 2),
+    round(agStressPerTiter(map)[4, "nd_excluded"], 2),
     1.67
   )
 
diff --git a/tests/testthat/test-map_merging.R b/tests/testthat/test-map_merging.R
index 02ddbebb..8486bdff 100644
--- a/tests/testthat/test-map_merging.R
+++ b/tests/testthat/test-map_merging.R
@@ -58,6 +58,20 @@ map2 <- acmap(
 titerTable(map2) <- titers2
 
 
+test_that("Merging maps with few optimizations", {
+
+  set.seed(850909)
+  many_dat <- replicate(3, acmap(
+    ag_names = paste0("A",1:10),
+    sr_names = paste0("S", 1:10),
+    titer_table = matrix(10*2^round(10*runif(100)), ncol=10)
+  ), simplify=F)
+
+  mmap <- mergeMaps(many_dat, method="reoptimized-merge", number_of_dimensions = 2, number_of_optimizations = 10)
+  expect_equal(numOptimizations(mmap), 10)
+
+})
+
 
 test_that("Antigens and sera match properly", {
 
diff --git a/tests/testthat/test-map_optimization.R b/tests/testthat/test-map_optimization.R
index 5673b3ed..fa712fb1 100644
--- a/tests/testthat/test-map_optimization.R
+++ b/tests/testthat/test-map_optimization.R
@@ -576,10 +576,29 @@ test_that("Error when optimizing a map with disconnected points", {
   dat[6:10,1:5] <- "*"
   dat[1:5,6:9] <- "*"
   map <- acmap(titer_table = dat)
-  expect_warning(
+  expect_error(
     optimizeMap(map, 2, 10, "none"),
-    no_cohesion_warning()
+    "Map contains disconnected points.*"
   )
 
 })
 
+
+# Errors for disconnected maps
+test_that("Optimizing a map with duplicate antigen or serum names", {
+
+  dat <- matrix(rep(40, 90), ncol=9)
+  ag_names <- rep("AG", nrow(dat))
+  sr_names <- rep("SR", ncol(dat))
+  rownames(dat) <- ag_names
+  colnames(dat) <- sr_names
+
+  map <- expect_warning(make.acmap(dat, number_of_optimizations = 2))
+  expect_equal(agNames(map), ag_names)
+  expect_equal(srNames(map), sr_names)
+  expect_equal(sum(is.na(agCoords(map))), 0)
+  expect_equal(sum(is.na(srCoords(map))), 0)
+
+})
+
+
diff --git a/tests/testthat/test-map_sequences.R b/tests/testthat/test-map_sequences.R
index 4ecb6495..ce4d88cf 100644
--- a/tests/testthat/test-map_sequences.R
+++ b/tests/testthat/test-map_sequences.R
@@ -26,9 +26,28 @@ test_that("Setting and getting sequences", {
 
 })
 
+test_that("Setting and getting nucleotide sequences", {
+
+  nucsequence <- matrix("a", nrow = numAntigens(map), ncol = 10)
+  agNucleotideSequences(map) <- nucsequence
+  expect_equal(nucsequence, agNucleotideSequences(map))
+
+  nucsequence_sr <- matrix("a", nrow = numSera(map), ncol = 6)
+  srNucleotideSequences(map) <- nucsequence_sr
+  expect_equal(nucsequence_sr, srNucleotideSequences(map))
+
+  tmp <- tempfile(fileext = ".ace")
+  save.acmap(map, tmp)
+  map_loaded <- read.acmap(tmp)
+  expect_equal(nucsequence,    agNucleotideSequences(map_loaded))
+  expect_equal(nucsequence_sr, srNucleotideSequences(map_loaded))
+
+})
+
 test_that("H3 map with sequences", {
 
   map <- read.acmap(test_path("../testdata/testmap_h3subset.ace"))
+
   agSequences(map) <- read.csv(
     file        = test_path("../testdata/testmap_h3subset_sequences.csv"),
     row.names   = 1,
@@ -48,6 +67,12 @@ test_that("H3 map with sequences", {
     check.names = FALSE
   )
 
+  map$antigens[[2]]$sequence <- substr(map$antigens[[2]]$sequence, 1, 40)
+  map$antigens[[3]]$sequence <- NULL
+
+  map$sera[[4]]$sequence <- substr(map$sera[[4]]$sequence, 1, 40)
+  map$sera[[6]]$sequence <- NULL
+
   export.viewer.test(
     view(map),
     "map_with_agsrsequences.html"
diff --git a/tests/testthat/test-map_strains.R b/tests/testthat/test-map_strains.R
index f57571e9..2d4e21f8 100644
--- a/tests/testthat/test-map_strains.R
+++ b/tests/testthat/test-map_strains.R
@@ -198,16 +198,20 @@ test_that("Getting and setting other attributes", {
   # Test defaults
   expect_equal(agExtra(map), rep("", numAntigens(map)))
   expect_equal(srExtra(map), rep("", numSera(map)))
+  expect_equal(srSpecies(map), rep("", numSera(map)))
 
   # Test editing
   ag_extras <- paste("AG EXTRA", seq_len(numAntigens(map)))
   sr_extras <- paste("SR EXTRA", seq_len(numSera(map)))
+  sr_species <- paste("SR SPECIES", seq_len(numSera(map)))
   agExtra(map) <- ag_extras
   srExtra(map) <- sr_extras
+  srSpecies(map) <- sr_species
 
   # Check changed values
   expect_equal(agExtra(map), ag_extras)
   expect_equal(srExtra(map), sr_extras)
+  expect_equal(srSpecies(map), sr_species)
 
   # Check saving and reloading
   tmp <- tempfile(fileext = ".ace")
@@ -216,6 +220,122 @@ test_that("Getting and setting other attributes", {
   loaded_map <- read.acmap(tmp)
   expect_equal(agExtra(loaded_map), ag_extras)
   expect_equal(srExtra(loaded_map), sr_extras)
+  expect_equal(srSpecies(loaded_map), sr_species)
+
+})
+
+# Getting and setting B lineage
+test_that("Getting and setting B lineage", {
+
+  # Read in the test map
+  map <- read.acmap(filename = test_path("../testdata/testmap.ace"))
+
+  # Test defaults
+  expect_equal(agLineage(map), rep("", numAntigens(map)))
+  expect_equal(srLineage(map), rep("", numSera(map)))
+
+  # Test editing
+  ag_lineage <- rep("V", numAntigens(map))
+  sr_lineage <- rep("Y", numSera(map))
+  agLineage(map) <- ag_lineage
+  srLineage(map) <- sr_lineage
+
+  # Check changed values
+  expect_equal(agLineage(map), ag_lineage)
+  expect_equal(srLineage(map), sr_lineage)
+
+  # Check saving and reloading
+  tmp <- tempfile(fileext = ".ace")
+  save.acmap(map, tmp)
+
+  loaded_map <- read.acmap(tmp)
+  expect_equal(agLineage(loaded_map), ag_lineage)
+  expect_equal(srLineage(loaded_map), sr_lineage)
+
+})
+
+# Getting and setting reassortant status
+test_that("Getting and setting reassortant status", {
+
+  # Read in the test map
+  map <- read.acmap(filename = test_path("../testdata/testmap.ace"))
+
+  # Test defaults
+  expect_equal(agReassortant(map), rep("", numAntigens(map)))
+  expect_equal(srReassortant(map), rep("", numSera(map)))
+
+  # Test editing
+  ag_reassortant <- rep("R", numAntigens(map))
+  sr_reassortant <- rep("R", numSera(map))
+  agReassortant(map) <- ag_reassortant
+  srReassortant(map) <- sr_reassortant
+
+  # Check changed values
+  expect_equal(agReassortant(map), ag_reassortant)
+  expect_equal(srReassortant(map), sr_reassortant)
+
+  # Check saving and reloading
+  tmp <- tempfile(fileext = ".ace")
+  save.acmap(map, tmp)
+
+  loaded_map <- read.acmap(tmp)
+  expect_equal(agReassortant(loaded_map), ag_reassortant)
+  expect_equal(srReassortant(loaded_map), sr_reassortant)
+
+})
+
+# Getting and setting boolean strings
+test_that("Getting and setting strings", {
+
+  # Read in the test map
+  map <- read.acmap(filename = test_path("../testdata/testmap.ace"))
+
+  # Test defaults
+  expect_equal(agStrings(map), rep("", numAntigens(map)))
+  expect_equal(srStrings(map), rep("", numSera(map)))
+
+  # Test editing
+  ag_strings <- rep("E", numAntigens(map))
+  sr_strings <- rep("C", numSera(map))
+  agStrings(map) <- ag_strings
+  srStrings(map) <- sr_strings
+
+  # Check changed values
+  expect_equal(agStrings(map), ag_strings)
+  expect_equal(srStrings(map), sr_strings)
+
+  # Check saving and reloading
+  tmp <- tempfile(fileext = ".ace")
+  save.acmap(map, tmp)
+
+  loaded_map <- read.acmap(tmp)
+  expect_equal(agStrings(loaded_map), ag_strings)
+  expect_equal(srStrings(loaded_map), sr_strings)
+
+})
+
+# Getting and setting ag continent
+test_that("Getting and setting continent", {
+
+  # Read in the test map
+  map <- read.acmap(filename = test_path("../testdata/testmap.ace"))
+
+  # Test defaults
+  expect_equal(agContinent(map), rep("", numAntigens(map)))
+
+  # Test editing
+  ag_continent <- rep("NORTH-AMERICA", numAntigens(map))
+  agContinent(map) <- ag_continent
+
+  # Check changed values
+  expect_equal(agContinent(map), ag_continent)
+
+  # Check saving and reloading
+  tmp <- tempfile(fileext = ".ace")
+  save.acmap(map, tmp)
+
+  loaded_map <- read.acmap(tmp)
+  expect_equal(agContinent(loaded_map), ag_continent)
 
 })
 
diff --git a/tests/testthat/test-plot_map.R b/tests/testthat/test-plot_map.R
index 043b3918..213a4359 100644
--- a/tests/testthat/test-plot_map.R
+++ b/tests/testthat/test-plot_map.R
@@ -21,6 +21,17 @@ test_that("Plotting a bare bones", {
 
 })
 
+# test_that("Plotting a 1D map", {
+#
+#   map <- optimizeMap(map, 1, 2, "none", check_convergence = F)
+#   export.plot.test(
+#     plot(map),
+#     "1dmap.pdf",
+#     8, 4
+#   )
+#
+# })
+
 test_that("Plotting a map with error lines", {
 
   map <- read.acmap(test_path("../testdata/testmap.ace"))
diff --git a/tests/testthat/test-underconstrained_positions.R b/tests/testthat/test-underconstrained_positions.R
index 772ccd38..55420874 100644
--- a/tests/testthat/test-underconstrained_positions.R
+++ b/tests/testthat/test-underconstrained_positions.R
@@ -20,7 +20,7 @@ test_that("Warn of undercontrained positions", {
     ),
     paste(
       "The following ANTIGENS have do not have enough titrations to position in 2 dimensions.",
-      "Coordinates were still optimized but positions will be unreliable\n\n'ANTIGEN 4'"
+      "Coordinates were still optimized but positions will be unreliable\n\n'A4'"
     )
   )
 
@@ -44,7 +44,7 @@ test_that("Error for underconstrained points with infinite positions", {
     ),
     paste(
       "The following ANTIGENS are too underconstrained to position in 2 dimensions",
-      "and coordinates have been set to NaN:\n\n'ANTIGEN 4'"
+      "and coordinates have been set to NaN:\n\n'A4'"
     )
   )
 
diff --git a/tests/testthat/test-view_map.R b/tests/testthat/test-view_map.R
index 4dc9c45a..ec47d523 100644
--- a/tests/testthat/test-view_map.R
+++ b/tests/testthat/test-view_map.R
@@ -4,6 +4,14 @@ context("Viewing a map")
 
 map <- read.acmap(test_path("../testdata/testmap.ace"))
 
+# Viewing a null map
+test_that("Viewing a 1D map", {
+
+  map <- optimizeMap(map, 1, 2, "none", check_convergence = F)
+  export.viewer.test(view(map), "map_1D.html")
+
+})
+
 # Viewing a null map
 test_that("Viewing a null map", {
 
@@ -298,6 +306,37 @@ test_that("Viewing map transparency", {
 
 })
 
+# Point opacity
+test_that("Viewing map with underconstrained points", {
+
+  set.seed(850909)
+  dat <- matrix(10*2^round(10*runif(100)), ncol=10)
+  for (i in 1:10){
+    dat[i,i:10] <- "*"
+  }
+  map <- expect_warning(make.acmap(dat, options = list(ignore_disconnected = TRUE)))
+  map2 <- expect_warning(make.acmap(dat[2:10,]))
+
+  widget1 <- view(map)
+  widget2 <- view(map2)
+
+  widget1 <- htmlwidgets::onRender(
+    x      = widget1,
+    jsCode = "function(el, x, data) { el.viewer.colorPointsByStress(); }",
+    data   = NULL
+  )
+
+  widget2 <- htmlwidgets::onRender(
+    x      = widget2,
+    jsCode = "function(el, x, data) { el.viewer.colorPointsByStress(); el.viewer.showErrorLines(); }",
+    data   = NULL
+  )
+
+  export.viewer.test(widget1, "map_ag_no_titers.html")
+  export.viewer.test(widget2, "map_ag_underconstrained.html")
+
+})
+
 
 # # Snapshot map
 # test_that("Map snapshot", {