Multigene-Phylogeny: How to merge several Multiple-Sequence-Alignments?
1
0
Entering edit mode
5.7 years ago
Tom.Ma • 0

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 RaxML Fasta MSA alignment • 5.0k views
ADD COMMENT
1
Entering edit mode

you may try concat from seqkit.

ADD REPLY
0
Entering edit mode

Thats been a good tip, thanks!

ADD REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode
5.7 years ago
Brice Sarver ★ 3.8k

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

ADD COMMENT

Login before adding your answer.

Traffic: 1436 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