Question: Estimating Neighbor Joining Tree using GTR model
gravatar for mm8511
4.3 years ago by
mm85110 wrote:

I am wondering if anyone can help me figure out how to build a neighbor joining tree in R, where the pairwise distances (from sequence alignments) are estimated under the GTR model. I have tried the dist.dna() method from R's phanghorn package, but it does not have support for the GTR model. I am new to phylogenetics, and any help would be great.

R phylogenetics nj gtr • 1.9k views
ADD COMMENTlink modified 4.3 years ago by Brice Sarver3.5k • written 4.3 years ago by mm85110
gravatar for Brice Sarver
4.3 years ago by
Brice Sarver3.5k
United States
Brice Sarver3.5k wrote:

While you can estimate distances under a handful of models in R, to my knowledge you are only able to estimate trees under the GTR model when using likelihood-based approaches (as, for example, in phangorn's optim.pml() and others). Unfortunately, I think you'll have to do this outside of R. Most sophisticated phylogenetic estimation isn't done in R, anyway.

I don't have time to skim through the PAUP manual and provide detailed instructionsl, but you can calculate distances under the GTR model and estimate a tree generally following this tutorial.

ADD COMMENTlink written 4.3 years ago by Brice Sarver3.5k

This is great. I really appreciate it

ADD REPLYlink written 4.3 years ago by mm85110
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1515 users visited in the last hour