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)
