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    • Philippe Veber's avatar
      orthomam: model choice for branch length calculation · 12a37ee9
      Philippe Veber authored
      see #11 for details:
      
      @boussau:
      > model with codon positions: iqtree -s orf1a_b_cds_NT_OK.fst -spp partitionFile.nex where partitionFile.nex contains :
      >
      > #nexus begin sets; charset part1 = 1-23070\3; charset part2 = 2-23070\3; charset part3 = 3-23070\3; charpartition mine = GTR+R:part1, GTR+R:part2, GTR+R:part3; end;
      >
      > where 23070 is the total size of the alignment It's a model that is a bit parameter rich, so don't use it on single gene alignments.
      >
      > For amino acids, I'd do: iqtree -s orf1a_b_cds_prot_OK.fst -m LG+F+R
      >
      > And for codons: iqtree -s orf1a_b_cds_NT_OK.fst -st CODON1 -m ECMK07+F
      12a37ee9
    • Philippe Veber's avatar
      5c88a750
  16. 16 Apr, 2020 1 commit