<commit_before># GCPSR (Genealogical Concordance Phylogenetic Species Recognition)

This package contains perl scripts for the implementation of the
genealogical concordance phylogenetic species recognition method.

## Prerequisites

You need to have perl 5 on your computer (on Mac and Linux this is by
default installed).

The scripts in this repository use the `Bio::Tree::Tree` package.

    # To install using cpan
    cpan Bio::Tree::Tree

## Perl scripts
<commit_msg>preprocessing<commit_after># GCPSR (Genealogical Concordance Phylogenetic Species Recognition)

This package contains perl scripts for the implementation of the
genealogical concordance phylogenetic species recognition method.

## Prerequisites

You need to have perl 5 on your computer (on Mac and Linux this is by
default installed).

The scripts in this repository use the `Bio::Tree::Tree` package.

    # To install using cpan
    cpan Bio::Tree::Tree

## Data preprocessing 

It is important to ensure that the right input trees are used for the
GCPSR analysis. The majority-rule consensus trees produced from single
locus phylogenies have to meet the following requirements:
- Trees are rooted using the same outgroup
- The outgroup contains at least two strains
- The clades have bootstrap (BS) or Bayesian posterior probability
  (BPP) support values 
- Support values appear as internal node names
  (e.g. _(((A,B)**80**,(C,D)**92**)**100**,(X,Y)**100**)_ or with
  branch lengths: _(((A:0.03,B:0.02)**80**:0.07,(C:0.04,D:0.01)**92**:0.05)**100**:0.10,(X:0.07,Y:0.04)**100**:0.2)_)
- Trees are in either **newick** ("`*.nwk`") or **nexus**
  ("`*.nex.*.t`" or "`*.nex.*.tre`") format and have one of the file
  extensions recognized by the scripts

## Perl scripts

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{'dir': 'git-commits-cleaned', 'id': '1708363', 'n_tokens_mistral': 573, 'n_tokens_neox': 503, 'n_words': 214}