Multigene-Phylogeny: How to merge several Multiple-Sequence-Alignments?
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2.8 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 • 2.6k views
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you may try concat from seqkit.

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Thats been a good tip, thanks!

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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.

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2.8 years ago
Brice Sarver ★ 3.7k

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

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