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Restore the use of MSA for phylogenetics

Workum, Dirk-Jan van requested to merge restore_msa_for_phylogenetics into develop

Since at least PanTools v4.2.0 (when pantools msa for various modes was completely separated), MSAs could technically not be used for phylogenetics anymore. The reason for this is that technically speaking one should do phylogenetics on nucleotide sequence alignments that were created by using the trimming from their corresponding proteins alignments. This is restored with this merge request that adds a flag --trim-using-proteins to pantools msa and implements code for this to trim nucleotide sequences based on a previous protein alignments prior to nucleotide alignment.

Still to do:

  • Update the way pantools core_phylogeny and pantools consensus_tree work as they depend on correct MSAs for phylogenetics.
  • Add the changes to CHANGELOG.md.
  • Add the changes to the documentation.
  • Fix the type of sequence extracted per mrnaNode (currently full mRNA is used for 'nuc' alignment whereas this should be only CDS).
Edited by Workum, Dirk-Jan van

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