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.
- Python 3
- TreeSwift
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>
-i
: Input newick tree file
-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).
python3 tag_decomp.py -i example/gtrees-mult.trees