v0.2.3

• Added test for shuffle sites
• Added --stable-rogues option to shuffle sites

v0.2.3b

• goalign sample rarefy: now checks sequence names
• Added option for nexus input and output
• goalign concat now adds gaps when a sequence is not present
• Corrected phylip parser
• Added unknown alphabet
• Added goalign sort command

v0.2.3a

• Added commands clean seqs and clean sites
• Changed Alignment GetSequence functions
• Added goalign sample rarefy command
• Corrected avg entropy computation

v0.2.2

• Correction : mutate snvs only on non gap positions
• Added --input-strict and --output-strict options for phylip input and output
• Added information on number of variable sites in goalign stats
• Modified documentation
• Added tests for goalign command line

v0.2.1

• Added goalign mutate snvs command to add uniform random noise (~sequencing errors) to an input alignment
• Renamed goalign shuffle gaps command to goalign mutate gaps

v0.2.0

• Added md documentation of goalign commands in docs folder
• Print logs on stderr for clean command
• Added shuffle gaps command
• Corrected sequence name in distance matrix output

v0.1.10

• Corrected average distance computation
• Changed command goalign sample to goalign sample seqs
• Added command goalign sample sites to extract a subalignment
• Added command goalign concat to concatenate several alignments

v0.1.9

• Authorize "." in sequences

v0.1.9-a

• New command goalign subseq to extract a subsequence from the alignment
• New normalization for goalign compute pssm to compute logo
• If two sequences have the same name, it will rename them and print a warning instead of exiting with an error

v0.1.8

• Added option --remove-gaps to command goalign compute entropy
• Added goalign compute pssm to compute pssm
• Corrected bug in fasta parser with windows end of lines.