Outgroup from command line

Question

[Lee Katz]

Hi Biostars, is there a command-line way to guess the best outgroup? Command-line tree-builders such as raxml can accept an outgroup as an argument but sometimes it is not something known a priori.

[Lee Katz]

I think that one thing that could be helpful, for example, is that I have a pairwise distance file with three tabs:

genome1  genome2  distance

And I have a perl script to total the distance although probably not optimized

perl -MList::Util=max -lane '
  $d{$F[0]}+=$F[2]; $d{$F[1]}+=$F[2]; # give distance 'points' to each genome
  $e{$d{$F[1]}}=$F[1]; $e{$d{$F[0]}}=$F[0]; # reverse-index which points belong to which genome
  END{
    $max=max(values(%d));   # find the max distance attributed to a genome
    print "$e{$max}\t$max"; # print the genome and its distance
  }
' < pairwise.tsv

However, I think that because of a sampling bias, it is not giving me the correct outgroup.

Answer 1

[David W]

For most software the tree seach uses unrooted trees, so the outgroup you set is of no consequence -- it just roots it at the end (section 10 of the raxml quickstart makes this clear, for instance).

You should just estimate you tree, then use mid-point rooting if it's important that you use rooted trees in down-stream analyses.

[Lee Katz]

Ok that makes sense, thank you!