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Commits on Nov 6, 2020

• add orthogroup gene count script

  davidemms

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• Locate previous WorkingDirectory if containing dir moved, resolves #476

  davidemms

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• Only write columns in HOG files for included species, resolves #475

  davidemms

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• Merge branch 'master' of https://github.com/davidemms/OrthoFinder

  davidemms

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• Use relative path for previous species tree if required, resolves #476

  davidemms

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• Continue HOG analysis on failure of a single tree

  davidemms

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Commits on Nov 5, 2020

• Adjust README formatting

  davidemms

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• Describe option for splitting (rare) paralogous clades at root of HOGs

  davidemms

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• Add command line options to README

  davidemms

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Commits on Nov 3, 2020

• Update README

  davidemms

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• Update README info on Hierarchical Orthogroups

  davidemms

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• Tidy up README

  davidemms

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Commits on Nov 2, 2020

• The FileHandler object shouldn't be used by multiple processes

  davidemms

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• Option to split paralogous clades below root of a HOG into separate HOGs

  davidemms

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Commits on Oct 28, 2020

• HOGs v3.1, extend dup evidence check to current node

  davidemms

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• HOGs v3, require evidence from both child clades for dup at NX

  davidemms

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Commits on Oct 27, 2020

• Remove unused code from old algorithm

  davidemms

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• Simplify HOG writer algorithm, resolves unwritten genes

  davidemms

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Commits on Oct 23, 2020

• HOG writer, edge cases

  davidemms

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• Increase HOG precision & recall: implied duplications

  davidemms

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• Refactor get_hogs_to_write

  davidemms

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Commits on Oct 22, 2020

• Prevent skipped HOGs one level down

  davidemms

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Commits on Sep 29, 2020

• Eliminate race condition in creating pickle dir, resolves #453

  davidemms

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Commits on Sep 17, 2020

• Allow analysis of DNA sequences

  davidemms

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Commits on Sep 1, 2020

• List expected filename extensions in README

  davidemms

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Commits on Aug 24, 2020

• Users will sometimes ignore stderr

  davidemms

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Commits on Aug 18, 2020

• Add info on config_orthofinder_user.json

  davidemms

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• Merge branch 'master' of https://github.com/davidemms/OrthoFinder

  davidemms

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• Allow an extra user config file in home directory, resolves #444

  davidemms

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Commits on Jul 28, 2020

• Update README on <4 taxa trees, resolves #433

  davidemms

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Commits on Jul 16, 2020

• Update README.md

  davidemms

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Commits on Jul 15, 2020

• Shrink image

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• Shrink image

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• Add image

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• Add description of Phylogenetically-Inferred Hierarchical Orthogroups results files

  davidemms

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