Perl scripts for analyzing polyploid DNA sequence data (Phylogenetics Of Linkage-Map-Anchored Polyploid Subgenomes)
MakeOneMapFromPileup.pl - reads a pileup file and converts it to OneMap format
MakeOneMapFromPileupNoParents.pl - similar to MakeOneMapFromPileup.pl, but assumes all samples are offspring, parent genotypes unknown.
MakeCharacterMatrix.pl - finds phylogenetic markers sharing sequence reads with linkage map markers
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