Question: Multigene-Phylogeny: How to merge several Multiple-Sequence-Alignments?
gravatar for Tom.Ma
18 months ago by
Tom.Ma0 wrote:

Hello, i'd like to build a multi-gene-tree of 14 fungal genomes. I did so far:

  • Analyze the protein-sequences of all genomes for shared orthologs using orthoMCL
  • Filter the resulting groups/clusters for those containing (only) one ortholog of every genome
  • Generate 299 separate Fasta-Files of those groups with the sequences of the orthologs
  • Run a MAFFT-alignment on every one of them separately

My files look like this one:

Grph|08566 ----------------RGAFEWAGNSVGGLFCQASNIVSPSHWRMVWDVVRFNYQSIASLRAFDRASEEQ---------------------------- Rany|05125 ----------------MRIAVIGSGVSGLAATWALNEAGNSVGGLFCQASNIVAGNSVGGLFCQASNIV----------------------------------- Acai|269125 ----------------MRIEWAGNSVGGLFCQATWALNEAGNSVGGLFCQASNIVAGNSVGGLFCQASNIV----------------------------

The order of the species (e.g. Grph) in those files is varying from file to file.

My next step would be, to run RaxML.

My question is: How do I combine those 299 separated alignments to get one "multi-gene-alignment" as Input for RaxML?

Thank you for your help.

mafft msa raxml alignment fasta • 1.2k views
ADD COMMENTlink modified 17 months ago by Brice Sarver3.5k • written 18 months ago by Tom.Ma0

you may try concat from seqkit.

ADD REPLYlink written 18 months ago by liupfskygre190

Thats been a good tip, thanks!

ADD REPLYlink written 18 months ago by Tom.Ma0

You can merge the MSAs 'end to end', and then with RAxML use a partition file (I think). The partition file is needed to demarcate where each alignment starts and ends.

Another option might be to compute a consensus/species tree from all of the gene trees via ASTRAL or similar.

ADD REPLYlink written 18 months ago by Joe17k
gravatar for Brice Sarver
17 months ago by
Brice Sarver3.5k
United States
Brice Sarver3.5k wrote:

I provided this solution for another question, but it will work just as well for combining MSAs: A: merge two multifasta files

ADD COMMENTlink written 17 months ago by Brice Sarver3.5k
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: 710 users visited in the last hour