GeMoMa-1.1.1 (01.02.2016)
- initial release for paper
GeMoMa-1.1.2. (05.02.2016)
- GeMoMa bugfix (upstream, downstream sequence for splice site detection)
- Extractor: new parameter s for selecting transcripts
- improved Galaxy integration
GeMoMa 1.1.3 (06.06.2016)
- minor modifications to the Extractor tool 
GeMoMa 1.3 (06.12.2016)
- ERE: new tool for extracting RNA-seq evidence
- Extractor: offers options for 
	- partial gene models
	- ambiguities
- GeMoMa:
	- RNA-seq
		- defining splice sites
		- additional feature in GFF and output
			- transcript intron evidence (tie)
			- transcript acceptor evidence (tae)
			- transcript donor evidence (tde)
			- transcript percentage coverage (tpc)
			- ...
	- improved GFF
	- simplified the command line parameters
	- IMPORTANT: parameter names changed for some parameters
- GAF: new tool for filtering and combining different predictions (especially of different reference organisms)
GeMoMa 1.3.1 (09.12.2016)
- GeMoMa bugfix (finding start/stop codon for very small exons) 
GeMoMa 1.3.2 (18.01.2017)
- Extractor: new parameter repair for broken transcript annotations
- GeMoMa: bugfixes (splice site computation)
GeMoMa 1.4 (03.05.2017)
- AnnotationEvidence: new tool computing tie and tpc for given annotation (gff)
- CompareTranscripts: new tool comparing predicted and given annotation (gff)
- Extractor:
	- reading CDS with no parent tag (cf. discontinuous feature)
	- automatic recognition of GFF or GTF annotation
	- Warning if sequences mentioned in the annotation are not included in the reference sequence
- GeMoMa: 
	- allowing for multiple intron and coverage files (= using different library types at the same time)
	- NA instead of "?" for tae, tde, tie, minSplitReads of single coding exon genes
	- new default values for the parameters: predictions (10 instead of 1) and contig threshold (0.4 instead of 0.9)
	- bugfix (write pc and minCov if possible for last CDS part in predicted annotation)
	- bugfix (ref-gene name if no assignment is used)
	- bugfix (minSplitReads, minCov, tpc, avgCov if no coverage available)
- GAF:
	- nested genes on the same strand
	- bugfix (if nothing passes the filter)
GeMoMa 1.4.1 (30.05.2017)
- CompareTranscripts: bugfix (NullPointerException)
- Extractor: reference genome can be .*fa.gz and .*fasta.gz
- GeMoMa: bugfix (shutdown problem after timeout)
- modified additional scripts and documentation
GeMoMa 1.4.2 (21.07.2017)
- automatic searching for available updates
- AnnotationEvidence: bugfix (tie computation: Arrays.binarysearch does not find first match)
- Extractor: bugfix (files that are not zipped)
- GeMoMa: bugfix (tie computation: Arrays.binarysearch does not find first match)