Genetics and population analysis SNAP: Combine and Map modules for multilocus population

Summary:Wehaveadded twosoftware tools to ourSuiteofNucleotide Analysis Programs (SNAP) for working with DNA sequences sampled frompopulations. SNAPMapcollapsesDNAsequencedata intounique haplotypes, extracts variable sites andmanipulates output intomultiple formats for input into existing software packages for evolutionary ana-lyses. Map collapses DNA sequence data into unique haplotypes, extracts variable sites and manipulates output into multiple formats for input into existing software packages for evolutionary analyses. Map includes novel features such as recoding insertions or deletions, including or excluding variable sites that violate an infinite-sites model and the option of collapsing sequences with corresponding phenotypic information, important in testing for significant haplotype–phenotype associations. SNAP Combine merges multiple DNA sequence align-ments into a single multiple alignment file. The resulting file can be the union or intersection of the input files. SNAP Combine currently reads from and writes to several sequence alignment file formats including both sequential and interleaved formats. Combine also keeps track of the start and end positions of each separate alignment file allowing the user to exclude variable sites or taxa, important in creating input files for multilocus analyses. Availability: SNAP Combine and Map are freely available a