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Commits on May 26, 2018

• Revisions to user guide in progress.

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Commits on Nov 1, 2017

• Starts release 3.2. Includes updates to documentation, tutorial.

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Commits on Jan 12, 2017

• clean up copyright type and dates.

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Commits on Aug 24, 2016

• Resolves issue #7. Saved MSAs (-A) now include name, desc, acc, author.

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Commits on Feb 22, 2015

• Updating documentation in preparation for 3.1b2 release. Other minor file

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Commits on Feb 21, 2013

• A variety of small output-related changes identified while modifying

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• Update tutorial files in preparation for H3.1b1 release.

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Commits on Feb 12, 2013

• nhmmer now accepts an alignment (or single sequence) as query input, as

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Commits on Feb 8, 2013

• New tutorial seed and model for nhmmer.

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Commits on Feb 3, 2013

• Beginning to prepare the nhmmer branch for release. This commit includes

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Commits on May 1, 2012

• Fairly meaty change to windowing in the long-target pipeline used by

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Commits on Mar 22, 2012

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Commits on Mar 17, 2012

• Preparing nhmmer alpha 0.25, and the some changes in nhmmer output

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Commits on Dec 1, 2011

• Recent windowing strategy changes rendered the nhmmer tutorial output example obsolete.

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Commits on Oct 7, 2011

• FM-index-based MSV filter in-progress. This code implements

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Commits on Jul 6, 2011

• updating the output file in the tutorial folder to agree with the new output resulting from the modified bias filter

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Commits on Jun 16, 2011

• Bugfix #h90: phmmer consensus line differs from query sequence. This

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Commits on May 23, 2011

• Adding files to the tutorial folder to be used with nhmmer:

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Commits on Mar 28, 2010

• Merged 3.0 release branch to trunk; updates to bugtrax, tutorial.

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Commits on Mar 12, 2010

• 3.0rc2 release cycle complete.

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Commits on Feb 10, 2010

• Changes from 3.0 (rc1) branch (3152:3161) merged back to trunk.

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Commits on Nov 15, 2009

• 3.0b3 release cycle complete.

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Commits on Oct 19, 2009

• Fixed bug #h60: hmmbuild --mpi fails to record GA,TC,NC thresholds.

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Commits on Jun 17, 2009

• Tutorial files and documentation updated for beta1.

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Commits on Jun 16, 2009

• bug #h55 fixed: hmmbuild was failing to deal gracefully with

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Commits on Jun 1, 2009

• hmmbuild.c: remove fake_tracebacks(), trace_doctor(); this

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Commits on Mar 13, 2009

• Preparing for HMMER3.0a2 release.

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Commits on Jan 12, 2009

• Finished drafting the alpha release user's guide.

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• Moved the old tutorial directory away to old-tutorial.

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Commits on Jan 6, 2009

• added h2_io.c: i/o of HMMER2 ASCII format.

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Commits on Oct 25, 2008

• Main changes summarized:

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Commits on May 23, 2003

• Alphabet now includes U for selenocysteine.

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Commits on May 7, 2003

• Still working on documentation.

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Commits on Apr 18, 2000

• unknown change, but it looks like a complete replacement

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• complete replacement, in updated MSF format

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