Matching Gene Trees in Treefile to Alignment File Names

[simone-says]

Is the order of the gene trees output in the *.treefile the same order that the alignment files are read in, or the same order that is output into the log file during partition testing? I need to match individual gene trees to the alignments that made them, but there are no unique identifiers preserved in the *.treefile.

This is the command used to make the gene trees:
iqtree2 -S /projects/busco_phylo/results/03_trimal/03_realigned_trim2/UCEs/05_unsat --prefix UCEs_unsat.loci -T AUTO

[roblanf]

@simone-says, they are in the same order as the

SEQUENCE ALIGNMENT
------------------

section of the .iqtree file. A simple way to confirm this if you have some trees with differening numbers of taxa is to cross-reference them that way (the table in the SEQUENCE ALIGNMENT section has taxon numbers).

Rob