Bioinformatics Advance Access published online on April 6, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl136
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1 Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695; Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695
* To whom correspondence should be addressed.
Summary: We have added two software tools to our application suite for working with DNA sequences sampled from populations. SNAP 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 indels, 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 alignments 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 at (http://snap.cifr.ncsu.edu/). These programs can be downloaded separately for Mac, Windows and Unix operating systems or bundled in SNAP Workbench. Each program includes online documentation and a sample dataset. Supplementary information: A description of system requirements and installation instructions can be found at http://snap.cifr.ncsu.edu/.
Received February 16, 2006
Revised March 31, 2006
Accepted April 4, 2006
Applications note
SNAP: Combine and Map modules for multilocus population genetic analysis
David L. Aylor 1,
Eric W. Price 2,
and
Ignazio Carbone 2 *
2 Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695
Ignazio Carbone, E-mail: ignazio_carbone{at}ncsu.edu
Abstract
Associate Editor: Martin Bishop
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