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

v0.3.3c

• Added option --char to goalign clean sites command (#5)
• Added --unique option to goalign mask (#5)
• Added --reverse option to goalign subseq (#7)
• Added goalign subsites command (#7)
• Added option --ref-seq to goalign mask (#6)