RuneBlaze / DISCO

Decomposition Into Single-COpy gene trees (DISCO) is a method for decomposing multi-copy gene-family trees while attempting to preserve orthologs and discard paralogs.

DISCO

Decomposition Into Single-COpy gene trees (DISCO) is a method for decomposing multi-copy gene-family trees while attempting to preserve orthologs and discard paralogs.

Dependencies

• Python 3
• TreeSwift

Usage

Input: File containing list of multi-copy trees in newick format

Output: File containing resulting list of single-copy trees after decomposition in newick format

python3 tag_decomp.py -i <input_file> -o <ouput_file> -d <delimiter>

Arguments

Required

• -i: Input newick tree file

Optional

• -o: Output newick tree file
• -d: Delimiter separating species name from rest of leaf label. Default None.
• -m: Output only single tree (discarding smallest duplicate clades).
• -n: No decomposition (outputs rooted gene trees).
• -v: Enable verbose output
• -rp: Remove in-paralogs before rooting/scoring (does not affect output, only reported score)
• --trivial: Includes trivial trees in decomposition output (by default trees not containing a quartet).
• --outgroups: Write outgroups (including ties) to txt file. (Might make program slower).

Example

python3 tag_decomp.py -i example/gtrees-mult.trees