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