changes in version 1.7.3 (2020-01-08)
- Include GenomeThreader related code from GenomeTools.
changes in version 1.7.2 (2020-01-06)
- Open-source release, no functionality changes.
changes in version 1.7.1 (2018-09-11)
- gthbssmtrain gives an error if no donor or acceptor sites were found.
changes in version 1.7.0 (2018-02-07)
- Update to libgenometools commit 161fb4c21ddf8f6f3a90c587816192592e7cdfa5.
- GenomeThreader is not protected by a license manager anymore.
changes in version 1.6.6 (2016-05-02)
- Update to libgenometools v1.5.8.
- Update to ZLM v1.10.
- Linux 64-bit versions are compiled with musl libc for better compatibility.
changes in version 1.6.5 (2014-11-05)
- gth has new option -cdnaforward (align only forward strand of cDNAs)
changes in version 1.6.4 (2014-10-29)
- Update to ZLM v1.7-prerelease.
- License files starting with an UTF-8 byte order mark (BOM) can be parsed.
changes in version 1.6.3 (2014-09-17)
- Update to ZLM v1.6.
changes in version 1.6.2 (2014-02-12)
- distribute only dynamically linked binaries which are very portable
- define the ambiguous amino acid 'J' (Leucine or Isoleucine) as wildcard
changes in version 1.6.1 (2013-09-18)
- Fix problem with impossible events in self-trained BSSMs.
- Update to ZLM v1.2.
- It is not necessary anymore to set the environment variables $BSSMDIR and
$GTHDATADIR, if the directories bssm/ and gthdata/ are in the same directory
as the executables.
changes in version 1.6.0 (2013-06-06)
- Change from RLM to ZLM (v1.0).
- GFF3 output: 5' splice sites now have the type 'five_prime_cis_splice_site'
(instead of 'five_prime_splice_site') and 3' splice sites the type
'three_prime_cis_splice_site' (instead of 'three_prime_splice_cite') to comply
with the new version of SOFA (Sequence Ontology Feature Annotation).
changes in version 1.5.2 (2012-06-10)
- The format for MD5 sequence IDs has changed (option -md5ids).
It now uses md5:063b1024d68e26716b7f38caf958316f:1877523 instead of
md5:063b1024d68e26716b7f38caf958316f. That is, the ``original'' sequence ID is
kept after the MD5 hash.
- Wrong source tag in GFF3 output has been fixed.
changes in version 1.5.1 (2012-06-05)
- fix bug in implementation of option -fastdp
- update to RLM v9.3 (BL2 - release date February 15, 2012)
changes in version 1.5.0 (2012-04-02)
- protein spliced alignments are computed with less memory
- update to RLM v9.2 (BL3 - release date October 21, 2011)
- allow to disable file locking with environment variable GTHNOFLOCK (set to any
value)
changes in version 1.4.9 (2011-09-17)
- update to RLM v9.1 (BL3 - release date May 2, 2011)
- gth and gthconsensus have new options -startcodon and -finalstopcodon
- gth has new options -enrichchains and -fastdp
- the PGL line in the (default) textual output now shows the genomic template.
Use the new option '-pglgentemplate no' disable this (for backward
compatibility)
changes in version 1.4.8 (2011-05-19)
- gthbssmtrain handles sequences containing wildcards (e.g., 'N') correctly
changes in version 1.4.7 (2011-03-02)
- gth has new option -duplicatecheck. The default value 'both' solves a problem
in GenomeThreader which could lead to falsely discarded spliced alignments.
To reproduce the behaviour in older GenomeThreader versions, use option
'-duplicatecheck id'. Please refer to the manual for details.
- gth and gthconsensus have new options -gff3out and -md5ids.
The GFF3 output is sorted. Please refer to the manual for details.
- gthbssmtrain shows number of processed gt-ag and gc-ag splice sites
- gthbssmtrain is described in Section 9 of the updated GenomeThreader manual
changes in version 1.4.6 (2011-02-05)
- new tool `gthbssmtrain` added: gthbssmtrain allows to generate custom splice
site probability files (the so-called BSSM files). Custom BSSM files are very
helpful to improve the quality of GenomeThreader gene structure predictions.
- handle additional codon translation tables
- GenomeThreader can handle Pyrrolysine ('O' in single letter code)
- update to RLM v9.0 (BL3 - release date Jan 5, 2011)
- GenomeThreader can handle the ambiguous amino acid 'J' (Leucine or Isoleucine)
- problem with fission_yeast.bssm file fixed
changes in version 1.4.5 (2010-07-20)
- gth is faster and needs less memory
changes in version 1.4.4 (2010-07-08)
- gthconsensus is much faster now, gth a little bit
changes in version 1.4.3 (2010-06-09)
- update to RLM v8.0 (BL6 - release date Jun 1, 2010)
changes in version 1.4.2 (2010-02-17)
- update to RLM v8.0 (BL3 - release date Jan 26, 2010)
changes in version 1.4.1 (2010-01-12)
- a bug in the protein spliced alignment computation has been fixed
changes in version 1.4.0 (2009-09-21)
- protein spliced alignments are computed much faster now (up to 3 times,
depending on your input data)