SNAP is a fast and accurate aligner for short DNA reads. It is optimized for modern read lengths of 100 bases or higher, and takes advantage of these reads to align data quickly through a hash-based indexing scheme.
Matei Zaharia, William J. Bolosky, Kristal Curtis, Armando Fox, David Patterson, Scott Shenker, Ion Stoica, Richard M. Karp, and Taylor Sittler. Faster and More Accurate Sequence Alignment with SNAP.
arXiv:1111.5572v1, November 2011.
SNAP calculates synonymous and non-synonymous substitution rates based on a set of codon-aligned nucleotide sequences. It outputs a synonymous and a non-synonymous distance matrix, an exhaustive pairwise codon-by-codon comparison, and a summary table.
Korber B. (2000)
HIV Signature and Sequence Variation Analysis.
Computational Analysis of HIV Molecular Sequences, Chapter 4, pages 55-72.
Allen G. Rodrigo and Gerald H. Learn, eds. Dordrecht, Netherlands: Kluwer Academic Publishers.
The SNaP program can be used to generate SNP haplotype sequence data of unrelated individuals and nuclear families with a fixed or random number of children.
SNAP is a web server for finding and annotating proxy SNPs based on linkage disequilibrium, genomic location, and coverage by commercial genotyping arrays.
SNAP (screening for non-acceptable polymorphisms) is a method for evaluating effects of single amino acid substitutions on protein function.SNAP identifies over 80% of the non-neutral mutations at 77% accuracy and over 76% of the neutral mutations at 80% accuracy at its default threshold. Each prediction is associated with a reliability index that correlates with accuracy and thereby enables experimentalists to zoom into the most promising predictions.
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.