SNAP: Combine and Map modules for multilocus population genetic analysis

• Published in: Bioinformatics 2006-06, Vol.22 (11), p.1399-1401
• Main Authors: Aylor, David L., Price, Eric W., Carbone, Ignazio
• Format: Article
• Language: English
• Subjects: Algorithms; Biological and medical sciences; Computational Biology - methods; Fundamental and applied biological sciences. Psychology; Gene Expression Profiling - methods; General aspects; Genetics, Population; Genomics - methods; Haplotypes; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Models, Genetic; Phenotype; Programming Languages; Sequence Alignment; Sequence Analysis, DNA - methods; Software
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btl136

We have added two software tools to our Suite of Nucleotide Analysis Programs (SNAP) 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 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 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 . 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. Contact:[e-mail] Supplementary information: A description of system requirements and installation instructions can be found at