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@rmhubley rmhubley released this Jan 9, 2020

Bugfix release

  • Work around a bug introduced in the new NCBI Blast 2.10.0 with version 5 databases.

  • RepeatScout in some rare cases will generate models for very long-period satellites. This can cause Refiner to go crazy creating tons of off-diagonal alignments. This version filters out these rare cases.

  • This version now prints out the version of each dependency in the log.

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@rmhubley rmhubley released this Nov 15, 2019 · 8 commits to master since this release

RepeatModeler 2.0 now supports LTR structural search using a combination of LTR_harvest and LTR_retriever.

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@rmhubley rmhubley released this Oct 20, 2017 · 97 commits to master since this release

Bugfix release. Avoid bailing if Refiner could not produce a consensus from the family sequence set.

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@rmhubley rmhubley released this May 12, 2017 · 103 commits to master since this release

  • Bugfix release. Fixes a bug that will cause RepeatModeler to exit if no new repeats are detected after round-2. In typical runs repeats will continue to be discovered even up to the last round and this bug will not be exercised.
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@rmhubley rmhubley released this Apr 6, 2017 · 106 commits to master since this release

  • RepeatModeler employs a genome sampling approach that is based
    on a random number generator. In this release of RepeatModeler
    we print out the random number generator seed at the start of
    a run. This number can be used with the "-srand ####" flag in future
    runs to exactly reproduce the samples taken from a given database.

  • The final output files are now placed in the same directory as
    the input database.

  • An additional output file is now generated containing the seed
    alignment for each discovered family. This alignment is the source
    of the final consnesus and is stored in a Dfam compatible Stockholm
    file. The new output files are named <database_name>-families.fa and
    <database_name>-families.stk.

  • Support for Dfam_consensus has been built into this release. Two
    utilities dfamConsensusTool.pl and renameIds.pl can be found in the
    RepeatModeler util/ directory. The dfamConsensusTool script enables
    one to upload curated seed alignments to the open Dfam_consensus
    database from the command line. The renameIds script simplifies
    the process of coming up with unique identifiers for a set of
    RepeatModeler generated families given a naming template.

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