Releases · evolbioinfo/goalign

New functionalities:

Simplot : Added command goalign compute simplot to generate similarity plot data and image
Mutation list : Added option --codon to goalign stats mutation list command (37eb44c , d79470b , c961992)
Extract sequence from the end : Added option for specifying negative lengths (-l --length) in goalign subseq command to extract alignment from the end (a3a0522)

Corrected a problem in goalign clean sites affecting the counts when --ignore-n was specified (d30c6e7)

Updated goalign codonalign , support remaining nucleotides with warning
Added command goalign replace stops: replace internal stop codons with NNN in nt sequences of input alignment
Added option goalign clean seqs --unaligned
Added command goalign mutate ambig: Add random N|X to sequences
Added command goalign reformat stockholm

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

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

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

@lucblassel

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

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