@davidemms davidemms released this Nov 8, 2018 · 12 commits to new_output_dir since this release

Assets 4

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

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

@davidemms davidemms released this Aug 31, 2018 · 56 commits to master since this release

Assets 4

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!

@davidemms davidemms released this May 21, 2018 · 60 commits to master since this release

Assets 4

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)

@davidemms davidemms released this Apr 11, 2018 · 71 commits to master since this release

Assets 4

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

@davidemms davidemms released this Mar 9, 2018 · 82 commits to master since this release

Assets 4

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

@davidemms davidemms released this Feb 19, 2018 · 94 commits to master since this release

Assets 4

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

@davidemms davidemms released this Nov 21, 2017 · 128 commits to master since this release

Assets 4

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

@davidemms davidemms released this Oct 1, 2017 · 167 commits to master since this release

Assets 4

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!

@davidemms davidemms released this Sep 12, 2017 · 199 commits to master since this release

Assets 4

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:

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

@davidemms davidemms released this Jun 14, 2017 · 218 commits to master since this release

Assets 4

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:

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