Perl scripts for analyzing polyploid DNA sequence data
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MakeCharacterMatricesWithInvariant.pl
MakeCharacterMatrix.pl
MakeOneMapFromPileup.pl
README.md

README.md

POLiMAPS

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