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hoelzer-lab / ribap

A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
GNU General Public License v3.0
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Estimate model per MSA and then design phylogeny run #38

Closed hoelzer closed 1 year ago

hoelzer commented 2 years ago

It makes more sense to estimate a substitution model per single RIBAP group (thus MSA) instead of a single model for the concatenated MSA or just using some default one.

This can be done via IQtree:

iqtree -s $ALN --mem 1G -T AUTO --threads-max 4 -nt 4 -m TEST -pre ${BN}-modeltest

Then, for each single MSA a model is estimated. Now, the model-MSA combination can be defined for inout of IQtree w/o the need of concatenating all MSAs into one big MSA.

http://www.iqtree.org/doc/Advanced-Tutorial check the section "Partitioned analysis with mixed data"

So you write a nexus file with the partition scheme and the alignment files can be specified in there too.

hoelzer commented 2 years ago

Related to general implementation of IQTree instead of RAxML #21

klamkiew commented 1 year ago

From the looks of it, iqtree generates single trees for each partition specified in the nexus file. Which means, in theory, we could ditch fasttree;

edit: wait a second though. I am currently just looking at MSAs part of the core genome. So, one would have to extend the iqtree step to all MSAs...

edit2: nevermind, I was looking at another output-directory :)