OrthoFinder v2.1.2

OrthoFinder version 2
Our next paper describing the new functionality will be out soon. Note, output files and default options could potentially change before the final version but results should stay the same

New to version 2:

• Improved orthologues from gene trees inference method: A new method has been implemented that replaces dlcpar as the default. The new method is both significantly faster and more accurate. This is achieved by focusing analysis only on nodes of the gene tree that affect orthologue inference (large trees now analysed in second rather than hours).
• The orthologue accuracy has been benchmarked with the community Quest for Orthologs service and the results can be seen on their website.
• Our newly published method, STRIDE: Species Tree Root Inference from Gene Duplication Events, has been integrated for rooting of the species tree.
• A new results table of all gene duplication events for each branch of the species tree is provided. The duplication events are cross-referenced to the gene trees, the support for each is quantified, and the ones meeting the stringent STRIDE checks are marked.
• Consider using the Diamond option instead of BLAST. The benchmarks show that the accuracy is similar (see link above) but DIAMOND is incredibly fast!

New to this release

• Performance improvements for large datasets
• Support compressed BLAST/DIAMOND results files
• MSA method for species tree
• Orthologue statistics

OrthoFinder v2.0.0-beta

New Version 2.0 beta release!
(Our next paper describing the new functionality will be out soon. Note, output files and default options could potentially change before the final version but all results should stay the same)

New:

• Improved orthologues from gene trees inference method: A new method has been implemented that replaces dlcpar as the default. The new method is both significantly faster and more accurate. This is achieved by focusing analysis only on nodes of the gene tree that affect orthologue inference (large trees now analysed in second rather than hours).
• The orthologue accuracy has been benchmarked with the community Quest for Orthologs service and the results can be seen on their website.
• Our newly published method, STRIDE: Species Tree Root Inference from Gene Duplication Events, has been integrated for rooting of the species tree.
• A new results table of all gene duplication events for each branch of the species tree is provided. The duplication events are cross-referenced to the gene trees, the support for each is quantified, and the ones meeting the stringent STRIDE checks are marked.
• Consider using the Diamond option instead of BLAST. The benchmarks show that the accuracy is similar (see link above) but DIAMOND is incredibly fast!

OrthoFinder v1.1.10

Recently Added Functionality:

• New SingleCopyOrthogroups.txt results file i.e. orthogroups containing only one-to-one orthologues relevant for cross-species comparisons.
• Allow any multiple sequence alignment and tree inference program to be used for inference of gene trees
• New MSA and tree inference tools can be user-added by adding a tool to the config.json file.
• Allow Diamond as a significantly faster alternative to BLAST search. Available on github.
• New Orthogroups.GeneCount.csv results file giving the number of genes per species in each orthogroup, allowing easy plotting of orthogroup results.
• Updated the manual.

Version 1.1.10: Resolved some minor issues since version 1.1.8

As of version 1, automated inference of:

• Orthologues (in addition to previously inferred orthogroups). See Orthogroups, Orthologues & Paralogues.
• Gene trees for all orthogroups
• Rooted species tree

There are extra dependencies need to perform the new (version 1) analyses, please see README file: https://github.com/davidemms/OrthoFinder

OrthoFinder v1.1.8

Added Functionality:

• New SingleCopyOrthogroups.txt results file i.e. orthogroups containing only one-to-one orthologues relevant for cross-species comparisons.
• Allow any multiple sequence alignment and tree inference program to be used for inference of gene trees
• New MSA and tree inference tools can be user-added by adding a tool to the config.json file.
• Allow Diamond as a significantly faster alternative to BLAST search. Available on github.
• New Orthogroups.GeneCount.csv results file giving the number of genes per species in each orthogroup, allowing easy plotting of orthogroup results.
• Updated the manual.

As of version 1, automated inference of:

• Orthologues (in addition to previously inferred orthogroups). See Orthogroups, Orthologues & Paralogues.
• Gene trees for all orthogroups
• Rooted species tree

There are extra dependencies need to perform the new (version 1) analyses, please see README file: https://github.com/davidemms/OrthoFinder

OrthoFinder v1.1.4

Additional functionality:

• Perform orthologue inference using gene trees inferred from multiple sequence alignments (requires MAFFT and FastTree)
• Add extra options to control which steps of workflow to perform: e.g. write sequence files for orthogroups

As of version 1, automated inference of:

• orthologues (in addition to previously inferred orthogroups)
• gene trees for all orthogroups
• rooted species tree

There are extra dependencies need to perform the new (version 1) analyses, please see README file: https://github.com/davidemms/OrthoFinder

OrthoFinder v1.1.2

Additional functionality:

• Orthologues inference using user-provided species tree
• Start orthologue inference from previous orthogroups or from previous trees

As of version 1, automated inference of:

• orthologues (in addition to previously inferred orthogroups)
• gene trees for all orthogroups
• rooted species tree

There are extra dependencies need to perform the new (version 1) analyses, please see README file: https://github.com/davidemms/OrthoFinder

OrthoFinder v1.0.8

New, automated inference of:

• orthologues (in addition to previously inferred orthogroups)
• gene trees for all orthogroups
• rooted species tree

There are extra dependencies need to perform the new analyses, please see README file: https://github.com/davidemms/OrthoFinder

Fix to standalone binary unable to run BLAST, DLCpar etc..

OrthoFinder v1.0.7

New, automated inference of:

• orthologues (in addition to previously inferred orthogroups)
• gene trees for all orthogroups
• rooted species tree

There are extra dependencies need to perform the new analyses, please see README file: https://github.com/davidemms/OrthoFinder

Fix to handle new command line format for dlcpar.

OrthoFinder v1.0.6

New, automated inference of:

• orthologues (in addition to previously inferred orthogroups)
• gene trees for all orthogroups
• rooted species tree

There are extra dependencies need to perform the new analyses, please see README file: https://github.com/davidemms/OrthoFinder

OrthoFinder v1.0.2-beta

New, automated inference of:

• gene trees for all orthogroups
• rooted species tree
• orthologues
  This is a beta release, if you are not interested in any of the new functionality you should download the previous non-beta version. There are two extra dependencies need to perform the new analyses (fastme & DLCpar), please see README file: https://github.com/davidemms/OrthoFinder

Updates: removed need for ete2, reduced package size, restructured output files.