Apr 182012
 

SNAP Workbench 2.0

:: DESCRIPTION

SNAP (Suite of Nucleotide Analysis Programs) Workbench is a Java program that manages and coordinates a series of analysis programs for making inferences on population processes. SNAP workbench allows the user to customize the implementation of complex console programs and functions for the purpose of automating and enhancing data exploration. In our implementation, the workbench facilitates population parameter estimation by ensuring that the assumptions and program limitations of each analysis method are met and by providing a step-by-step methodology to effectively integrate both summary-statistic methods and coalescent-based population genetic models.

SNAP Map is a command line-based tool that 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 is a command-line based tool that merges the contents of multiple single locus DNA sequence files into a single multi-locus output file. There are various input and output file formats. The files can be merged into a union or intersection of all the input loci. Additionally Combine tracks the start and end positions of each file allowing the user to exclude variable sites or taxa, important in creating input files for multilocus analyses.

::DEVELOPER

the Carbone lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • Java
:: DOWNLOAD

  SNAP Workbench

:: MORE INFORMATION

Citation

Aylor, D. L., Price, E.W. and I. Carbone. 2006.
SNAP: Combine and Map modules for multilocus population genetic analysis.
Bioinformatics 22:1399-1401.

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