===================== 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