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updating header in concatenate.py

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Auden Cote-L'Heureux 2025-01-19 11:06:23 -05:00 committed by GitHub
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PTL2/Scripts/concatenate.py
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@ -1,12 +1,12 @@
# Last updated Jan 2024 # Last updated Jan 2024
# Authors: Auden Cote-L'Heureux and Mario Ceron-Romero # Authors: Auden Cote-L'Heureux and Mario Ceron-Romero
# This script chooses orthologs to concatenate OGs. This can be done as part of an end-to-end PhyloToL run, # This script chooses orthologs to concatenate OGs. This can be done as part of an end-to-end EukPhylo run,
# or by inputting already complete alignments and gene trees and running only the concatenation step. # or by inputting already complete alignments and gene trees and running only the concatenation step.
# Use the --concatenate flag to run this step, and optionally use the argument --concat_target_taxa to input # Use the --concatenate flag to run this step, and optionally use the argument --concat_target_taxa to input
# a file containing a list of taxon codes to be included in the concatenated alignment. If a GF has more # a file containing a list of taxon codes to be included in the concatenated alignment. If a GF has more
# than one sequence from a taxon, a representative ortholog must be chosen to include in the concatenated alignment. # than one sequence from a taxon, a representative ortholog must be chosen to include in the concatenated alignment.
# To do this, for each taxon PhyloToL keeps only the sequences falling in the monophyletic clade in the tree # To do this, for each taxon EukPhylo keeps only the sequences falling in the monophyletic clade in the tree
# that contains the greatest number of species of the taxon’s minor clade (or major clade, if the ‘target taxon list’ # that contains the greatest number of species of the taxon’s minor clade (or major clade, if the ‘target taxon list’
# uses major-clade codes). If multiple sequences from the taxon fall into this largest clade, then the sequence # uses major-clade codes). If multiple sequences from the taxon fall into this largest clade, then the sequence
# with the highest ‘score’ (defined as length times k-mer coverage for transcriptomic data with k-mer coverage # with the highest ‘score’ (defined as length times k-mer coverage for transcriptomic data with k-mer coverage