Perl scripts for analyzing polyploid DNA sequence data
MakeCharacterMatrix.pl - finds phylogenetic markers sharing sequence reads with linkage map markers
MakeOneMapFromPileup.pl - reads a pileup file and converts it to OneMap format
MakeCharacterMatricesWithInvariant.pl - finds phylogenetic markers sharing sequence reads with linkage map markers; includes all sites even invariants sites and creates a separate matrix for each reference genome chromosome