=====================
 PGDSpider Changelog
=====================
2.1.1.5 - 20180507
- bug fix (NEXUS writer)

2.1.1.4 - 20180503
- bug fix (FASTA parser)

2.1.1.3 - 20171110
- bug fix (VCF writer, MEGA parser)

2.1.1.2 -20170719
- bug fix (VCF parser)

2.1.1.1 -20170607
+ FASTA writer: option to write haploid sequences
- bug fix (MEGA parser)

2.1.1.0 - 20170116
+ new input formats: extended multi-FASTA format (XMFA), MAF
+ new output formats: extended multi-FASTA format (XMFA)
+ RAxML: support to parse/write partition file
+ integrate compatibility with samtools/bcftools >= 1.0
- bug fix (MIGRATE writer)

2.1.0.3 - 20160628
- bug fix (CLI spid file)

2.1.0.2 - 20160613
+ IM/IMA2/MEGA parser: option to keep loci separate or not
- bug fix

2.1.0.1 - 20160425
+ Arlequin writer: if too many SNPs collapse them
- bug fix (config file)

2.1.0.0 - 20160222
+ PGD format change: new sub tag "locusAncestralState" in locus tag to store ancestral state of locus
+ integrate locus ancestral state in VCF/BCF/SAM/BAM/Eigensoft parser and VCF/BCF/Eigensoft/Arlequin writer
+ Arlequin writer: numeric DNA encoding with 0 representing the ancestral state (SFS analyses)
- bug fix (VCF/BCF writer)

2.0.9.2 - 20160114
+ option to remove half missing genotypes in Bayenv writer
+ option to write sample/loci name file in Bayenv writer
- bug fix (missing data in binary NEXUS)

2.0.9.1 - 20151217
+ adapted Arlquin format
+ parse inter-marker distances (STRUCTURE)
- bug fix (Bayenv)

2.0.9.0 - 20150925
+ new output format: Bayenv

2.0.8.3 - 20150707
- bug fix (BAPS parser)

2.0.8.2 - 20150429
- bug fix (PHYLIP writer, VCF parser)

2.0.8.1 - 20150417
+ support for pop names in FASTA parser

2.0.8.0 - 20150311
+ support for SNP data in PHYLIP and MEGA writer
- bug fix (VCF parser)

2.0.7.4 - 20150127
- bug fix (NEXUS parser)
- bug fix (EIGENSOFT writer)

2.0.7.3 - 20150112
- bug fix (NEXUS parser)

2.0.7.2 - 20141010
- bug fix (EIGENSOFT format)
- bug fix (FASTA SNP parser)

2.0.7.1 - 20140815
- bug fix (Nexus binary format)

2.0.7.0 - 20140714
+ support for fastSTRUCTURE

2.0.6.0 - 20140702
+ new input formats: Stanford HGDP format, Eigensoft(EIGENSTRAT, ANCESTRYMAP), ONeSAMP
+ new output formats: Eigensoft(EIGENSTRAT, ANCESTRYMAP), BAMOVA, ONeSAMP, Structurama
+ new feature in BCF, FASTA, NEXUS, VCF
+ keep order of populations/individuals/loci
- bug fix

2.0.5.2 - 20140311
- bug fix

2.0.5.1 - 20131018
- SPID file bug fix

2.0.5.0 - 20130719
+ improved handling of indels in VCF and BCF parser
+ option to include non-polymorphic positions in VCF and BCF parser
- bug fix

2.0.4.0 - 20130221
+ NEXUS parser now able to parse CharSet/CharPartition commands in SET and MrBayes block
+ enhanced support for multi-locus DNA data
+ STRUCTURE writer able to output inter-marker distances

2.0.3.0 - 20130111
+ new features in FSTAT, GDA, GENEPOP, GENETIX, GESTE/BayeScan, IMMANC, NewHybrids and STRUCTURE writer
+ Arlequin frequency data is directly converted to STANDARD data type

2.0.2.1 - 20121204
- bug fix

2.0.2.0 - 20121030
+ vcf 4.1 support

2.0.1.9 - 20120828
+ new features in several parser/writer
- bug fix

2.0.1.8 - 20120810
+ memory error message

2.0.1.7 - 20120522
- bug fix

2.0.1.6 - 20120507
+ new input/output format: IMa2
+ new feature in PHYLIP format parser/writer

2.0.1.5 - 20120410
- bug fix

2.0.1.4 - 20120116
- bug fix

2.0.1.3 - 20111230
+ new feature in VCF/BCF format parser

2.0.1.2 - 20111207
+ new feature in PED format parser
- bug fix

2.0.1.1 - 20111109
- bug fix

2.0.1.0 - 20111010
+ new input/output format: FASTQ
+ new "Create/Edit SPID file" button
+ display "writing output file" information
+ file chooser: remember last directory
+ Java Web Start of PGDSpider 

2.0.0.3 - 20110617
+ new input/output formats: SAM, BAM, VCF,
  BCF, PED, GENELAND, NewHybrids

2.0.0.2 - 20091113
+ added cli mode
+ italian translation
+ new output formats: KML and GESTE/BayeScan

1.0.1.4 - 20081109
+ progress information during parsing process

1.0.1.3 - 20081104
+ french translation
+ change gui language without restart
- fixed memory issues in file viewer

1.0.1.2 - 20081103
+ language dependent help files

1.0.1.1 - 20081030
+ save window size on program exit
+ multi-language support

1.0.1.0 - 200810
- fixed windows loader for large file processing
  VM options "-Xmx1024m -Xms512M"

1.0.0.0 - 200809
- first release


__________________________________________________________
CMPG - Computational and Molecular Population Genetics Lab
Institute of Ecology and Evolution
University of Bern

Member of the Swiss Institute of Bioinformatics (SIB)

(c) 2007 - 2014 by Heidi Lischer, University of Bern

heidi.lischer@iee.unibe.ch
http://cmpg.iee.unibe.ch