Pairwise distance matrix with nucleotide substitution model
1
0
Entering edit mode
3.7 years ago

Dear community,

I have a sequence alignment (full 16S rDNA) and I'd like to calculate the sequence pairwise distance matrix using a nucleotide substitution model. The task could be easily achieved with the dist.dna() function of the R'package ape but there are not a lot of evolutionary model included (at least not the one I need). Indeed, screening my alignment with jModelTest I got that the best nucleotide substitution model for my data is TVM+I+G (invariable sites and rate variation among sites, respectively).

Does anyone know how I can get a distance matrix computed using this (TVM+I+G) substitution model?

Many thanks!

Luca

distance matrix substitution model TVM+I+G 16S • 1.7k views
ADD COMMENT
1
Entering edit mode
3.7 years ago

I eventually find out the solution. I report it in case someone might need it. jModelTest provides for the best solution the parameters (e.g. base frequency, gamma and proportion of invariable sites) to perform the related maximum likelihood analysis in PAUP (now available for free at http://paup.phylosolutions.com/). The parameters have to be specified when calling "Lset".

In my case the commands in PAUP were:

Executemy_align.nex
Lset base=(0.2167 0.2409 0.2804) nst=6 rmat=(1.0169 3.1065 1.6336 0.9465 3.1065) rates=gamma shape=0.5980 ncat=4 pinvar=0.1260
Dset distance=ml
ADD COMMENT

Login before adding your answer.

Traffic: 1815 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6