v0.1.5

• Added cutoff option to goalign clean command

v0.1.4

• "goalign subset" can take a regexp to select sequences
• added "goalign clean" command to remove gap sites
• added "goalign stats alleles" command to count average number of alleles per sites
• added option to "goalign compute distance" command, to display only average distance
• Correction:
  • Accept lower case nucleotides for distance computation
  • Corrected tests
  • Corrected Makefile

v0.1.3

• Added reformat nexus command to convert to nexus format
• subset command can now remove given sequences instead of keeping only them
• subset command can take a list in command line arguments
• Added addid command to append a string to all sequence names of an alignment
• Added random command to generate an random alignment
• Corrected bugs:
  • Authorize lower case characters
  • Corrected new lines in Fasta output

v0.1.2

• Added new commands:
  • goalign reformat tnt : Reformat an input alignment as input file for
  • goalign build tntweightboot: Builds bootstrap alignments with "continuous" weights, in input format
  • goalign stats taxa : Prints index and name of all taxa in an input alignment file
  • goalign subset : Take a subset of sequences from an alignment file
• Bug correction:
  • Corrected fasta writer
• Other:
  • Changed gamma distribution to Dirichlet distribution for weights

v0.1.1

v0.1.1