v0.3.3b

• Corrected translate function
• Added option --count-profile to goalign stats --per-sequeces, goalign stats gaps and goalign stats mutations to compare sequences to a profile (already computed with goalign stats char --per-sites)

v0.3.3a

• Added support for IUPAC characters for translatecommand
• Added --ref-seq option to goalign subseqto give coordinate based on a given sequence
• Added consensuscommand (simple majority consensus)
• Added goalign stats gaps and goalign stats mutations commands
• Added option --per-sequences to stats char command
• Added option --unaligned to sample seqs, sample rarefy and goalign replace commands
• Added goalign append command to concatenate alignments vertically
• goalign compute distance takes into account ambigous IUPAC characters for nucleotide distance computation (counting one mutation if characters are incompatibles, such as R and Y for example)

v0.3.2

• Added split command to split an alignment in several partitions
• Possibility to use partitions in bootstrap replicates

v0.3.1

• Corrected phylip parser (for multi alignments file)
• Corrected Nexus Parser when no alignment present in the input
• Corrected Clustal Parser
• Corrections with distances and models (added HIVB Model, more generic code for probabilities, etc.)
• Added --ignore-identical option (removes sequences with same sequence and same name, otherwise renames them)
• dedup writes identical sequence names in a log file
• dedup can take unaligned sequences
• reformat fasta can take unaligned sequences
• stats char can take several alignments
• stats nseq can take unaligned sequences
• subset can take sequence indices as input
• sample seq can generate several samples

v0.3.1-alpha2

• Implementation of aa sequence distances
• nt Evolutionary models
• Added --gap-mut option to compute distance command
• Added --alpha option to compute distance command
• Corrected output file index in unalign command
• Added --ends option to clean sites command
• Corrected Nexus Parser

v0.3.1-alpha

• Corrected phylip parser
• Corrected phase command
• Changed Makefile and test.sh
• Added diff command to compare all sequences to the first one
• stats taxa, sort and shuffle seqs work on unaligned file
• Repository transferred to evolbioinfo
• Added compress command to remove duplicate alignment patterns/sites
• Added vertebrate and invertebrate mitochondrial genetic codes (translate and phase commands)

v0.3.0

• Added goalign replace command
• goalign rename command can clean names and handle unaligned sequences
• goalign stats alphabet can handle unaligned sequences

v0.3.0-alpha5

• Added phase and phasent commands
• Added sw alignment
• Added orf command
• Added mask command
• Possibility to use unaligned sequences in : addid, stats length, orf, phase, phasent, subset, sw, translate
• Added options --no-block and --one-line to phylip writer
• Modified draw biojs options
• Phylip parser corrections
• Added a character to remove in clean names
• build bootstrap : Set n threads to 1 when seed is given

v0.3.0-alpha

• Added bash/zsh completion
• Go 1.10.3
• Added dedup command to remove duplicate sequences
• Changed trim seq command line option --from-start,-s to --from-left,-l
• Changed seed option, now only --seed for all commands
• Corrected exit status / exit points
• Added a "console" mode, when goalign is called without any arguments
• Changed alignment data structure using anonymous fields
• Added sub-command alphabet to command stats
• Added command codonalign to align a given nucleotide fasta file using a corresponding protein alignment
• Added command ìdentical` to assess whether two alignments are identical

v0.2.9

• Added support for Clustal format as input/output
• Added goalign translate function
• Added goalign stats maxchar command
• Added --per-site option to goalign stats char command
• goalign rename can now take a regex to substitute substrings in sequence names
• Giving an output mapping file is not mandatory anymore for goalign trim name command
• Changed nexus parser to accept numeric sequence names