Added biallelic option

[BobLiterman]

Previous (-s) option allowed for choice of Singletons vs. No Singletons. -s now has 3 options:

0 [Default]: All variable sites considered in 'loci' (alignment.nex) 1: No singletons (alignment_pi.nex) 2: Biallelic only (alignment_bi.nex)

changeMissing now partitions data subsets into separate folders (alignmentDataWithoutSingletons; alignmentDataWithOnlyBiallelic) and 'loci' will read from whichever dataset the user requests via -s.

[BobLiterman]

Also changed output of alignments.

• alignment.nex is all sites
• alingment_pi.nex excludes singletons
• alignment_bi.nex excludes singletons and 3+ allelic sites

[BobLiterman]

Changed changeMissing.py to report basic statistics about how many sites are lost after filtering for missing taxa.

[BobLiterman]

[BobLiterman]