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Commits on Dec 31, 2020

• updated aai_wf when using BLASTp to account for inteface changes in BioLib

  donovan-h-parks

  committed
  047d8e9

Commits on Mar 11, 2020

• Updated shebange to explicitly require Python 3.

  donovan-h-parks

  committed
  1cf30a4

Commits on Mar 2, 2020

• Updated setup.py for Py3 version of BioLib.

  donovan-h-parks

  committed
  3422a5e

Commits on Aug 25, 2018

• Merge branch 'master' of github.com:dparks1134/CompareM

  donovan-h-parks

  committed
  f226829

• minor updates

  donovan-h-parks

  committed
  38c25d0

Commits on Aug 18, 2018

• update to work on py3

  ctb

  committed
  bb00ded

Commits on Aug 4, 2017

• Fix to percent identity and alignment length filtering when using BLASTP.

  donovan-h-parks

  committed
  294195f

Commits on Jul 14, 2016

• Updates for DIAMOND v0.8.14 and added User's Guide.

  donovan-h-parks

  committed
  d23a540

Commits on Jul 4, 2016

• Removed high_mem option. Changes for DIAMOND v0.8.10.

  donovan-h-parks

  committed
  719b0a0

Commits on Jun 29, 2016

• Improved classify workflow, output of LGT commands, and help menu.

  donovan-h-parks

  committed
  8140a12

Commits on Jun 24, 2016

• Removed use of Cython. Changes to use DIAMOND >= 0.8.5. Improved interface.

  donovan-h-parks

  committed
  b6109ea

Commits on May 1, 2016

• Improvemnets to substantially reduce computation time.

  donovan-h-parks

  committed
  e01378b

Commits on Apr 28, 2016

• Fix bug with proper extraction of genome identifiers.

  donovan-h-parks

  committed
  1a1e43d

Commits on Apr 27, 2016

• Improved logger output and compatibility with biolib.

  donovan-h-parks

  committed
  bb0bc49

Commits on Apr 26, 2016

• Better logging.

  donovan-h-parks

  committed
  e7aee49

• Fixes to aai_wf.

  donovan-h-parks

  committed
  235a1c0

• Refined AAI calculation to better handle prefixing gene IDs and filtering on query coverage.

  donovan-h-parks

  committed
  ad8f12a

Commits on Aug 4, 2015

• added in ability of cluster the heatmap

  ctSkennerton

  committed
  476591f

Commits on May 26, 2015

• Minor edits to heatmap display; fixed issue with improper call to new biolib blast interface

  donovan-h-parks

  committed
  0eb40d2

Commits on May 22, 2015

• Added in a heatmap plotting subcommand

  ctSkennerton

  committed
  5908bc9

Commits on May 19, 2015

• Moved to compatibility with biolib v0.0.4.

  donovan-h-parks

  committed
  8b27004

Commits on Apr 6, 2015

• Merge branch 'master' of github.com:dparks1134/CompareM

  donovan-h-parks

  committed
  633968e

• Major update.

  donovan-h-parks

  committed
  d532f2e

• clarified help

  donovan-h-parks

  committed
  9f5d321

Commits on Feb 22, 2015

• Added KmerUsage(), LgtCodon(), and LgtDinucleotide() classes.

  donovan-h-parks

  committed
  68bf044

Commits on Feb 14, 2015

• Moved over to biolib.

  donovan-h-parks

  committed
  e99b217

Commits on Feb 13, 2015

• Added method for detecting putative LGT events.

  donovan-h-parks

  committed
  c7bac14

Commits on Feb 12, 2015

• Bug fix in SeqIO().read_seq() was causing last sequence to be missed.

  donovan-h-parks

  committed
  77e6273

Commits on Feb 10, 2015

• Improved use of Parallel class. Added class to run Diamond in parallel.

  donovan-h-parks

  committed
  d620792

Commits on Feb 9, 2015

• Improved Parallel() class. Updated AA and codon usage to use new Parallel() class.

  donovan-h-parks

  committed
  c6a423a

Commits on Feb 8, 2015

• Moved all files to underscore naming. Added "to do" lists to many classes.

  donovan-h-parks

  committed
  a2279ad

Commits on Feb 5, 2015

• Renamed folders from aai to comparem

  donovan-h-parks

  committed
  000a5ad

• Initial renaming from aai to comparem

  donovan-h-parks

  committed
  2b750e4

• Major update. Moving repository over to CompareM.

  donovan-h-parks

  committed
  13c35cc

Commits on Nov 19, 2014

• Major bug fix causing incorrect AAI calculations.

  donovan-h-parks

  committed
  258f7ce

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