How to calculate the distance estimation for amino acid?

[lqhungpt]

Hi Admin,
Can you give me the command line or how to estimate the distance matrix for amino acid with JTT model? I want to print out this matrix in output file.
Hung

[bqminh]

just run

iqtree2 -s ALN_FILE -m JTT

IQ-TREE will print a file with suffix ".mldist". This is the distance matrix under JTT model.
Note that this run will also infer a tree. If you only want to get the distance, you can speed up by adding -te BIONJ option:

iqtree2 -s ALN_FILE -m JTT -te BIONJ

It will only compute .mldist and the distanced based BIONJ tree, which is much faster for large alignment.

[lqhungpt]

Thank you, Prof. Bui. Can you show me how to estimate the F84 distance model with aligned nucleotide?
Hung

[roblanf]

Hi @lqhungpt

F84 is equivalent to HKY in terms of the parameterisation, i.e. a transition/transversion rate and unequal base frequencies.

So, you can do:

iqtree2 -s ALN_FILE -m HKY

Another option is to use model selection to find a model which best fits the data (including not just the structure of the Q matrix like GTR or HKY, but also the distribution of rates across sites, like +G, +I+G, +R etc).

To do that, followed by tree estimation:

iqtree2 -s ALN_FILE -m MFP

Hope that helps,

Rob