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)

GeMoMa 1.5 (13.02.2018)
- AnnotationEvidence: add chromosome to output
- CompareTranscripts: new parameter that allows to remove prefixes introduces by GAF
- Extractor: new parameter "stop-codon excluded from CDS" that might be used if the annotation does not contain the stop codons
- ExtractRNASeqEvidence: 
	- print intron length stats
	- include program infos in introns.gff3
- GeMoMa:
	- new attribute pAA in gff output if query protein is given
	- include program infos in predicted_annotation.gff3
	- minor bugfix
- GAF:
	- new parameter that allows to specify a prefix for each input gff
	- collect and print program infos to filtered_prediction.gff3
	- improved statistics output

GeMoMa 1.5.2 (31.5.2018)
- GAF:
	- new parameter that allows to restrict the maximal number of transcript predictions per gene
	- altered behavior of the evidence filter from percentages to absolute values
	- bugfix: nested genes 
	- checking for duplicates in prediction IDs
- GeMoMa:
	- warning if RNA-seq data does not match with target genome
- GeMoMaPipeline: new tool for running the complete GeMoMa pipeline at once allowing multi-threading
- folder for temporary files of GeMoMa

GeMoMa 1.5.3 (23.07.2018)
- improved parameter description and presentation
- GeMoMaPipeline:
	- removed unnecessary parameters 
- GeMoMa:
	- bugfix: reading coverage file
	- removed parameter genomic (cf. Extractor)
	- removed protein output (cf. Extractor) 
- GAF:
	- bugfix: prefix 
- Extractor:
	- new parameter genomic 
	
GeMoMa 1.6 (02.04.2019)
- allow to use mmseqs as alternative to tblastn
- AnnotationEvidence:
	- allows to add attributes to the input gff: tie, tpc, AA, start, stop
	- new parameter for gff output
- AnnotationFinalizer: new tool for predicting UTRs and renaming predictions
- GAF:
	- relative score filter and evidence filter are replaced by a flexible filter that allows to filter by relative score, evidence or other GFF attributes as well as combinations thereof
	- sorting criteria of the predictions within clusters can now be user-specified
	- new attribute for genes: combinedEvidence
	- new attribute for predictions: sumWeight
	- allows to use gene predictions from all sources, including for instance ab-initio gene predictors, purely RNA-seq based gene prediction and manually curation
	- bugfix for predictions from multiple reference organisms
	- improved statistic output
- GeMoMa
	- renamed the parameter tblastn results to search results
	- new parameter for sorting the results of the similarity search (tblastn or mmseqs), if you use mmseqs for the similarity search you have use sort 
	- new parameter for score of the search results: three options: Trust (as is), ReScore (use aligned sequence, but recompute score), and ReAlign (use detected sequence for realignment and rescore)
	- bugfix: threshold for introns from multiple files

GeMoMa 1.6.1 (04.06.2019)
- createGalaxyIntegration.sh: bugfix for GeMoMaPipeline
- new module CheckIntrons: allowing to create statistics for introns (extracted by ERE)
- AnnotationFinalizer: bugfix for sequence IDs with large numbers
- CompareTranscripts: 
	- bugfix for prefix of ref-gene
	- allow no transcript info, but making assignment non-optional if a transcript info is set  
- GAF: bugfix for Galaxy integration
	- bugfix for filter using specific attributes if no RNA-seq or query proteins was used
- GeMoMaPipeline:
	- improved output in case of Exceptions
	- new parameter "output individual predictions" allows to in- or exclude individual predictions from each reference organism in the final result
	- new parameter "weight" allows weights for reference species (cf. GAF)
- ERE: new parameter "minimal mapping quality"

GeMoMa 1.6.2 (17.12.2019)
- Jstacs changes:
	- test methods for modules
	- live protocol for Galaxy
- new module Denoise: allowing to clean introns extracted by ERE
- new module NCBIReferenceRetriever: allowing to retrieve data for reference organisms easily from NCBI.
- GAF:
	- bugfix for filter using specific attributes if no RNA-seq or query proteins was used
	- allow to add annotation info (as for instance provided by Phytozome) based on the reference organisms
- GeMoMa: bugfix for timeout
- GeMoMaPipeline:
	- bugfix reporting predicted partial proteins
	- improved protocol
	- new default value for query proteins (changed from false to true)
	- new default value for Ambiguity (changed from EXCEPTION to AMBIGUOUS)
	
GeMoMa 1.6.3 (05.03.2020)
- Jstacs changes:
	- CLI: bugfix ExpandableParameterSet
- python wrapper (for *conda)
- updated tests.sh, run.sh, pipeline.sh
- renamed Denoise to DenoiseIntrons
- AnnotationEvidence: write phase (as given) to gff
- GAF: new parameter: default attributes allows to set attributes that are not included in some gene annotation files
- GeMoMa: new parameter: static intron length allowing to use dynamic intron length if set to false
- GeMoMaPipeline: 
	- bugfix: time-out
	- improve output
	- separate parameters for maximum intron length (DenoiseIntrons, GeMoMa)
	
GeMoMa 1.6.4 (24.04.2020)
- improved help section
- change gff attribute "AA" to "aa"
- GAF:
	- bugfix overlapping genes
	- accelerated computation
- GeMoMa:
	- bugfix: if no assignment file is used and protein ID are prefixes of other protein IDs
	- change GFF attribute AA to aa
- AnnotationFinalizer: new parameter "name attribute" allowing to decide whether a name attribute or the Parent and ID attributes should be used for renaming