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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.
- 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 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 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.