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

GeMoMa 1.7. (29.07.2020)
- improved manual including new module and runtime 
- check whether input files exist before execution
- partially checking MIME types in CLI before execution
- changed homepage from http to https
- new module AddAttribute: allows to add attributes (like functional annotation from InterProScan) to gene annotation files that might be used in GAF or displayed genome browsers like IGV or WebApollo
- new module SyntenyChecker: creates a table that can be used to create dot plots between the annotation of the target and reference organism
- changed default value of parameter "tag" from "prediction" to "mRNA"
- AnnotationEvidence:
	- additional attributes: avgCov, minCov, nps, ce
	- changed default value of "annotation output" to true
	- bugfix: transcript start and end
- ERE: 
	- changed default value of coverage to "true" 
	- new parameter "minimum context": allows to discard introns if all split reads have short aligned contexts
- Extractor: 
	- bugfix splitAA if coding exon is very short
	- improved verbose mode
	- new parameter "upcase IDs"
	- new parameter "introns" allowing to extract introns from the reference (only for test cases)
	- new parameter "discard pre-mature stop" allowing to discard or use transcripts with pre-mature stop
	- improved handling of corrupt annotations
- GAF: 
	- bugfix missing transcripts
	- slightly changed the default value of "filter"	
- GeMoMa:
	- replaced parameter "query proteins" by "protein alignment"
	- using splitAA for scoring predictions 
	- new gff attributes: 
		- ce and rce for the feature prediction indicating the number of coding exons for the prediction and the reference, respectively
		- nps for the number of premature stop codons (if avoid stop is false)
	- slightly changed the meaning of the parameter "avoid stop"
- GeMoMaPipeline:
	- changed the default value of tblastn to false, hence mmseqs is used as search algorithm
	- changed the default value of score to ReAlign
	- remove "--dont-split-seq-by-len" from mmseqs createdb
	- new optional parameter BLAST_PATH
	- new optional parameter MMSEQS_PATH
	- new option to allow for incorporation of external annotation, e.g., from ab-initio gene prediction
	- new parameter restart allowing to restart the latest GeMoMaPipeline run, which was finished without results, with very similar parameters, e.g., after an exception was thrown (cf. parameter debug)

GeMoMa 1.7.1 (07.09.2020)
- GeMoMa: 
	- bugfix if assignment == null
	- bugfix remove toUpperCase
- GeMoMaPipeline
	- Galaxy integration bugfix for hidden parameter restart
	- hide BLAST_PATH and MMSEQS_PATH from Galaxy integration
	- improved protocol output if threads=1
	- add addtional test to GeMoMaPipeline