OrthoFinder v2.3.8

• Add support for Python 3 (continues to support Python 2.7)

OrthoFinder v2.3.7

Improvements:

• OrthoFinder now includes all it's dependencies so you should be able to just download it, unpack it and run
• Identify species-specific orthogroups
• Automatically root trees in 'Gene_Trees' directory and include support values if available (trees in 'Resolved_Gene_Trees' directory were already rooted)

Fixes:

• Resolve issue with Sophos causing final ortholog inference step to take a very long time (Issue #294)
• Resolve MMseqs issue with long sequences (>65535 AA) (Issue #269)
• Improve parallelisation of DendroBLAST gene trees
• Fix writing of phylogenetically misplaced genes to file (Issue #288)
• Skip missing trees for STAG (Issue #293)

OrthoFinder v2.3.3

• New, redesigned and clearer results directory structure
• Bug fixes for previous beta release

The results directory created by OrthoFinder has been redesigned to make it a lot clearer to see where all the results files, there are a lot of them now!

Results_Nov08/
  Comparative_Genomics_Statistics/
  Gene_Duplication_Events/
  Gene_Trees/
  Orthogroups/
  Orthogroup_Sequences/
  Orthologues/
  Resolved_Gene_Trees/
  Single_Copy_Orthologue_Sequences/
  Species_Tree/
  Log.txt

The binary package OrthoFinder-2.3.3.tar.gz has been built to use GLIBC 2.27. If you have an older system it may not support this, in which case you can use OrthoFinder-2.3.3_glibc-2.19.tar.gz, which should work on any current Linux distribution.

Fixes:

• Fix labelling of nodes in resolved gene trees so that they correctly correspond to gene duplication events listed in the Duplications.tsv file.
• Add option '-X' to deactivate inclusion of species name in the gene IDs.
• Print any error messages from DIAMOND/BLAST to enable identification of problems in input FASTA files.
• Use a larger test alignment file to prevent errors from raxml-ng.
• If extending a previous analysis, make no changes to files in previous directory.

OrthoFinder v2.3.1 (beta)

New, redesigned and clearer results directory structure

The results directory created by OrthoFinder has been redesigned to make it a lot clearer to see where all the results files, there are a lot of them now!

Results_Nov08/
  Comparative_Genomics_Statistics/
  Gene_Duplication_Events/
  Gene_Trees/
  Orthogroups/
  Orthogroup_Sequences/
  Orthologues/
  Resolved_Gene_Trees/
  Single_Copy_Orthologue_Sequences/
  Species_Tree/
  Log.txt

DIAMOND is now the default for the all-v-all search, replacing BLAST. It is many times faster with little change in accuracy.

This is a beta release. The latest stable release is v2.2.7 below.

OrthoFinder v2.2.7

New to this release

• Added support for MMseqs2, use '-S mmseqs' for faster all-versus-all sequence search
• Added support for RAxML-NG, use '-M msa -T raxml-ng'

OrthoFinder version 2
The next paper describing the new functionality will be out soon.

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.
• The species tree inference method has been updated, "STAG: Species Tree Inference from All Genes"
• 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 v2.2.6

OrthoFinder version 2
The next paper describing the new functionality will be out soon.

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.
• The species tree inference method has been updated, "STAG: Species Tree Inference from All Genes"
• 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

• Fix for resolving of non-binary gene trees
• Detect if lack of RAM has caused parallel OrthoFinder processes to be killed
• Fix to only check for required species in user species tree (don't check for excluded species)

OrthoFinder v2.2.3

OrthoFinder version 2
The next paper describing the new functionality will be out soon.

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.
• The species tree inference method has been updated, "STAG: Species Tree Inference from All Genes"
• 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

• Fixes to allow resolving of non-binary gene trees

OrthoFinder v2.2.1

OrthoFinder version 2
The next paper describing the new functionality will be out soon.

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.
• The species tree inference method has been updated, "STAG: Species Tree Inference from All Genes"
• 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

• Fixes to allow fewer than 4 species and to deal with species trees that are not fully resolved

OrthoFinder v2.2.0

OrthoFinder version 2
The next paper describing the new functionality will be out soon.

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.
• The species tree inference method has been updated, "STAG: Species Tree Inference from All Genes"
• 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 and RAM improvements for large datasets
• Identify horizontally transferred genes
• Improved rooting of gene trees
• Improved identification of orthologues from gene trees

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