v0.3.8

• New option --alphabet to all goalign commands( #14 - 13b116b)
• New option --pos to goalign shuffle swap (bdfb55a and 3eda576)
• New option swap to goalign shuffle recomb (c13a469)
• Updated the way Dirichlet samples are generated (4d18587)
• New option to revcomp only given sequences in goalign revcomp (f5c7c76)
• New command goalign toupperand tolower (264f3b8)
• New option n-as-gap for command goalign dedup (27d6175)
• Added support for Stockholm format (#15 - 05d8e38 and e80c26d)
• Updated clustal parser (dfefef7)
• Added gap=- in nexus output format line (44beac3)
• Updated goalign codonalign: if 3 nucleotides are remaining : ok with warning about potential stop codon (f4a9aab)
• Updated go to 1.21.6

v0.3.7

• Added option --aa to goalign stats mutations list
• Added option--reverse to goalign clean sites
• Added multi characters to option --char of goalign clean sites
• goalign extract supports '-' strand sequences
• Added option --ref-seq option to goalign translate and goalign extract --translate
• Added option --posfile to goalign replace: to replace specific characters at specific positions of specific sequences in an input alignment
• Added AB model (https://doi.org/10.1093%2Fmolbev%2Fmsu340)
• Updated LG model
• Added option -l to goalign concat to keep information of the coordinates of all input alignments in the concatenated alignment

v0.3.6

• Added option --no-gaps to goalign mask
• Added option --no-ref to goalign mask
• Added option --positions-rm to goalign clean sites
• Added option --pos to goalign mask
• Added command goalign mutations list to output a list of mutations compared to a reference sequence
• Added option --gff to goalign extract to take sequences to extract from a gff file
• Update go to 1.19

v0.3.6a

• Added command goalign draw png (thanks @lucblassel #11 !)
• Added compressed output (gz or xz) (#12 )
• Updated go to 1.18.3

v0.3.5

• Switched to go 1.16.4
• Corrected biojs dependency (for goalign draw)
• Updated citation
• Updated go.mod

v0.3.4

• Changed --ignore-identical behavior to differentiate identical names from identical names+sequences
• Added option --nb-sequences to goalign divide command
• Added option --unaligned to goalign trim name

v0.3.4a

• Corrected translate function
• Added support of xz and bz input alignments
• Added options --ignore-gaps and --ignore-n to commands clean seqs, clean sites, consensus and stat maxchars
• Switched from dep to go modules
• Modified RemoveMajorityCharacterSites & RemoveCharacterSites functions
• Added goalign revcomp command
• Added options --ref-seq, --at-most and --replace to goalign mask command

v0.3.3f

• Added goalign transpose command #9

v0.3.3e

• Added option -f/--frac to goalign build seqboot and goalign build distboot

v0.3.3d

• Corrected mask doc #6
• Added ignore case to clean seqs and clean sites and --char to clean seqs
• Corrected SubAlign + Added goalign extract command
• Added --informative option to goalign subsites to select informative sites
• Data structure optimization, rune to uint8
• Added option --rm-ambiguous in compute dist -m pdist command
• Added options --range1 and --range2 to goalign compute distance
• Added output positions to goalign clean sites
• Added option --consecutive to goalign sample sites