OGFilter is a script that parses the OrthoFinder output and returns only the orthogroups that meet specific criteria.
These criteria include:
- Minimum number of species present in orthogroup
- Maximum number of gene copies per species in orthogroup
This feature is particularly useful in phylogenomics analysis, where a researcher is interested in obtaining genes with high species representation but low multiple copy occurences.
| Argument | Description |
|---|---|
| -g filename | file w/ gene counts (from OrthoFinder output) |
| -s dirname | directory that contains the orthogroups fasta files (from OrthoFinder output) |
| -o dirname | directory to write the output orthogroups |
| -min_species float | minimum proportion of the original species in the desired orthogroups |
| -max_copies int | maximum number of gene copies per species in the desired orthogroups |
python OGFilter.py -g Orthogroups.GeneCount.tsv -s Orthogroup_Sequences -o output_dir -min_species 0.8 -max_copies 3
This will create an output directory (-o output_dir) which will contain all orthogroups with at least 80% of the original species present (-min_species 0.8) and with maximum 3 copies per species (-max_copies 3).
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Who
Mattia Giacomelli (mattia.giacomelli@bristol.ac.uk);
Paschalis Natsidis (p.natsidis@ucl.ac.uk);
Where
Pisani Lab, Uni Bristol;
Telford Lab, UCL;
ITN IGNITE;
When
November 2019;