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@davidemms davidemms released this Jan 6, 2021

New in this release

Added option to use DIAMOND ultra-sensitive: "-S diamond_ultra_sens". This identifies homologs for approximately 2% more genes, depending on how closely the input species are related.

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@davidemms davidemms released this Nov 30, 2020

New in this release

  • Significant speed improvements for large analyses
    • For analyses of ~200 species total run times are 2-4x faster
    • Parallelisation of final ortholog inference stage of algorithm (number of threads is controlled using "-a" option)
    • For MSA tree inference OrthoFinder performs light trimming of the MSA. This prevents the runtime being dominated by tree inference for the largest orthogroups with very gappy MSAs.
    • The tree inference using multiple sequence alignments option ("-M msa") is now comparable in speed to the default DendroBLAST method.
Assets 5

@davidemms davidemms released this Nov 6, 2020

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.
Assets 5

@davidemms davidemms released this Jul 15, 2020

New in this release

Phylogenetically inferred orthogroups: OrthoFinder now creates a new directory that contains orthogroups defined at each level in the species tree. These orthogroups are inferred by examining the gene trees using the same algorithm that OrthoFinder uses to infer orthologs. Because they are inferred by analysing gene trees they are substantially more accurate than any other method available (and give an approximately 10% relative increase in accuracy on the Orthobench benchmarks compared to OrthoFinder version 2). These files are in the new results directory Phylogenetic_Hierarchical_Orthogroups/.

Because OrthoFinder now infers orthogroups at each phylogenetic level within the species tree it is now possible to include outgroup species in your analysis. Then, to see the orthogroups for just your species of interest just use the corresponding file from the Phylogenetic_Hierarchical_Orthogroups/. The clade names N1, N2, etc. can be found in Species_Tree/SpeciesTree_rooted_node_labels.txt. The use of outgroup species can further increase accuracy (~13% relative increase compared to OrthoFinder v2).

Hierarchical orthogroups are useful because, due to gene duplication events, orthogroups become more fine grained as the species become more closely related:
Hierarchical Orthogroups

This is the first of a two part series of developments to increase OrthoFinder orthogroup accuracy using the analysis of gene trees.

Which package to download:

  • On Linux download OrthoFinder.tar.gz. This bundles all the required external dependencies (mcl, diamond, fastme) and python libraries and so should run immediately, without any installation being required.
  • On Mac the bioconda package is probably the easiest method: See Bioconda getting started and, once bioconda is set up, run conda install orthofinder
  • On either platform you can run the source code version but you will need to have python and the numpy & scipy libraries installed.
  • On Windows the best way is to install the Windows Subsystem for Linux and then use the linux version
    More detailed instructions here: https://davidemms.github.io/orthofinder_tutorials/alternative-ways-of-getting-OrthoFinder.html
Assets 4

@davidemms davidemms released this Jul 15, 2020

This is a stable release that fixes any known issues in the previous release.

Which package to download:

  • On Linux download OrthoFinder.tar.gz. This bundles all the required external dependencies (mcl, diamond, fastme) and python libraries and so should run immediately, without any installation being required.
  • On Mac the bioconda package is probably the easiest method: See Bioconda getting started and, once bioconda is set up, run conda install orthofinder
  • On either platform you can run the source code version but you will need to have python and the numpy & scipy libraries installed.
  • On Windows the best way is to install the Windows Subsystem for Linux and then use the linux version
    More detailed instructions here: https://davidemms.github.io/orthofinder_tutorials/alternative-ways-of-getting-OrthoFinder.html

Issues resolved

  • 'taskset' was previously used to resolve a problem with CPU affinity affecting python multiprocessing. This should no longer be an issue and has been removed.
  • Issue warning and continue if MSA fails, resolves #407
  • Fix to allow new directory in current directory, resolves #403
Assets 4

@davidemms davidemms released this May 7, 2020

This is a stable release that fixes any known issues in the previous release.

Which package to download:

  • On Linux download OrthoFinder.tar.gz. This bundles all the required external dependencies (mcl, diamond, fastme) and python libraries and so should run immediately, without any installation being required.
  • On Mac the bioconda package is probably the easiest method: See Bioconda getting started and, once bioconda is set up, run conda install orthofinder
  • On either platform you can run the source code version but you will need to have python and the numpy & scipy libraries installed.
  • On Windows the best way is to install the Windows Subsystem for Linux and then use the linux version
    More detailed instructions here: https://davidemms.github.io/orthofinder_tutorials/alternative-ways-of-getting-OrthoFinder.html

Issues resolved

  • Update primary_transcript.py for python3, resolves #345
  • Vectorise alignment trimming, 45mins->1.5s on 6 species x 3 million base alignment
  • Updates to Manual & README
  • Set OPENBLAS_NUM_THREADS=1, resolves #356
  • Fix reporting of external program error messages
  • Exception.message deprecated in python3, resolves #375
  • Correct handling of species tree without support values, resolves #379
  • Improve handling of commented out species
  • Check at start if open file limit is too low and inform user, resolves #384
Assets 4

@davidemms davidemms released this Feb 11, 2020

Which version to download:

  • On Linux download OrthoFinder.tar.gz. This bundles all the required external dependencies (mcl, diamond, fastme) and python libraries and so should run immediately, without any installation being required.
  • On Mac the bioconda package is probably the easiest method: See Bioconda getting started and, once bioconda is set up, run conda install orthofinder
  • On either platform you can run the source code version but you will need to have python and the numpy & scipy libraries installed.

New in this release

  • Resolve an issue in some situations when using OrthoFinder on Mac using bioconda. OrthoFinder would find mcl/diamond but would then be unable to call them when required.
  • Binary package (OrthoFinder.tar.gz) is now built for glibc versions 2.15 onwards for wider compatibility
Assets 4

@davidemms davidemms released this Feb 6, 2020

  • Bug fixes for upgrade to Python 3
  • Default package is now built for glibc versions 2.15 onwards for wider compatibility
Assets 4

@davidemms davidemms released this Nov 28, 2019

  • Add support for Python 3 (continues to support Python 2.7)
Assets 5

@davidemms davidemms released this Oct 22, 2019

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)
Assets 5