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Releases: Dfam-consortium/RepeatModeler

RepeatModeler 2.0.5

04 Oct 16:57
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  • Fixed a bug that caused failures in "absolute" reproducibility. Prior
    to this release use of the "-srand" would not gaurantee that the ouputs
    consensi.fa.classified and families-classified.stk were exactly the same
    in sequence and sequence order. It did gaurantee that the same samples
    were drawn from the genome, and that equivalent scoring families were
    derived at at each step. In this release secondary sorts were added
    to gaurantee a fixed sort order among equally scoring results, generating
    exactly the same output files each time the random number generator seed
    is used. NOTE: This change only applies to results generated with
    this version and future releases.
  • Added "-long" option to faToTwoBit to support larger genomes.

RepeatModeler 2.0.4

29 Nov 22:30
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  • Improved the gathering of RepeatScout examplars for building
    seed alignments.
  • Parallelized and improved the masking between rounds for faster
    runs and fewer redicoveries.
  • The 'pa' (parallel batches) option has been replaced with a new
    'threads' option which maps directly to the maximum number of
    threads the program will attempt to use.
  • Takes advantage of RepeatMasker 4.1.4 and RMBlast 2.13.0 parallel
    query feature.
  • Larger default sample sizes are now possible with speed improvements.
    The original sampling strategy can be selected with the new 'quick'
  • ABBlast is no longer supported.
  • Fixed a few visual artifacts in the html

RepeatModeler 2.0.3

08 Feb 18:58
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  • The program now generates a logfile in the working directory named
    -rmod.log. This file contains the random seed number used
    and some high level stats on the run for use with reporting problems
    with the program.
  • Fixed a problem with the orientation/coordinates provided in the
    Stockholm output format that affected a subset of the sequences.
  • Fixed a bug affecting the trim functions of the Linup tool.

RepeatModeler 2.0.2

30 Apr 18:04
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  • First release of a set of manual curation tools for use with de-novo generated TE libraries.
  • Added to generate Dfam compatible seed alignments given a consensus based TE library and RepeatMasker output.
  • Fixed bug in N50 calculation.
  • Fixed Ruzzo-Tompa maximal scoring subsequences implementation.
  • Several minor bugfixes.

RepeatModeler 2.0.1

09 Jan 23:55
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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.

RepeatModeler 2.0

15 Nov 23:54
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RepeatModeler 2.0 now supports LTR structural search using a combination of LTR_harvest and LTR_retriever.

RepeatModeler open-1.0.11

20 Oct 19:14
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Bugfix release. Avoid bailing if Refiner could not produce a consensus from the family sequence set.

RepeatModeler open-1.0.10

12 May 21:52
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  • 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.

RepeatModeler open-1.0.9

06 Apr 17:05
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  • 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

  • Support for Dfam_consensus has been built into this release. Two
    utilities and 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.