OrthoMerge

Python 3 pipeline to compare and merge orthology inference results of OrthoMCL, OrthoFinder and OrthoInspector

OrthologyMerge.py

Requirements:

• BioPython

Use: python3 OrthologyMerge.py -p <phylum> --orthomcl <OrthoMCL_groups> --orthofinder <OrthoFinder_groups> --orthoinspector <OrthoInspector_groups> -fd <FASTA_directory>

Input:

• orthologous groups output from OrthoMCL, OrthoFinder and OrthoInspector (all in OrthoMCL output format)
• phyla definitions in phyla.txt file in the following format: <phylum>:<species1>,<species2>[...] <superphylum>:<phylum>|<phylum>
• phylum of interest (must be defined in phyla.txt)

Output:

• log file containing numbers of groups inferred congruently between methods (default name: OrthologousGroups_identical+split.log)
• directory containing merged results of all orthology inference methods (default name: OrthologousGroups_identical+split)

OG_monophyly_test.py

Requirements:

• BioPython
• BLAST+
• Clustal Omega
• RAxML-NG
• DendroPy

Use: python3 OG_monophyly_test.py -od <OrthoGroups_directory> -db <sequence_database>

Input:

• directory containing orthogroups inferred as congruently inferred by OrthologyMerge.py
• database containing non-clade sequences to search for potential homologous sequences outside clade of interest
• optional: e-value for BLAST search (-e <e-value>, default: 10)

Output:

• text file containing the results of the monophyly test (default name: OrthologousGroups_monophyly.txt)
• directory containing BLAST results for each orthogroup
• directory containing all orthogroups without BLAST hits
• directory containing all orthogroups with BLAST hits including found hits and reconstructed gene trees

OG_rBBH_test.py

Requirements:

• BioPython
• BLAST+
• DendroPy

Use: python3 OG_rBBH_test.py -od <OrthoGroups_directory> -hd <BLAST_hits_directory> -m <Monophyly_test_results> -dbd <sequence_database_directory>

Input:

• directory containing orthogroups inferred as congruently inferred by OrthologyMerge.py
• directory containing all orthogroups with BLAST hits including found hits and reconstructed gene trees
• text file containing the results of the monophyly test
• directory containing BLAST databases for each individual species present in orthogroups

Output:

• text file containing the results of the rBBH test (default name: OrthologousGroups_rBBH.txt)
• directory containing BLAST results for each orthogroup (default name: OrthologousGroups_rBBHits)