OrthoFinder v2.4.1

New in this release

• Improvements to the accuracy of phylogenetically inferred hierarchical orthogroups (HOGs)
• Allow config_orthofinder_user.json as an extra config file in user's home directory to allow user-specific options and carrying user options between releases
• Allow analysis of nucleotide sequences with -d option
• Resolve #453
• Resolve #475
• Resolve #476

Details

• Orthogroups are now inferred using gene trees and are found in Phylogenetic_Hierarchical_Orthogroups/N0.tsv etc. The original OGs inferred using clustering are still in Orthogroups/Orthogroups.tsv, but the N0.tsv orthgroups are ~12% more accurate and should be used instead.
• The accuracy can be increased still further (20% more accurate on Orthobench) by including outgroup species, which help with the interpretation of the rooted gene trees. The species tree should then be used to identify the correct HOG file, N??.tsv according to the correct node of the species tree.
• It is important to ensure that the species tree OrthoFinder is using is accurate so as to maximise the accuracy of the HOGs. To reanalyse with a different species tree use the options -ft PREVIOUS_RESULTS_DIR -s SPECIES_TREE_FILE. This runs just the final analysis steps "from trees" and is relatively quick.
• Further accuracy increases can be obtained by using a lower MCL inflation value (e.g. -I 1.3) since this brings more genes into the gene trees, and the HOG algorithm will split the hierarchical orthogroups if required. On Orthobench this gives ~2% increase in accuracy.