SilVA 1.1.1 – Silent Variant Analysis using random Forests

SilVA 1.1.1

:: DESCRIPTION

SilVA (Latin for “forest”) is a tool for the automated harmfulness prediction of synonymous (silent) mutations within the human genome. SilVA bases its predictions on a number of features, including conservation, codon usage, splice sites, splicing enhancers and suppressors, and mRNA folding free energy. Given variants in a VCF file, SilVA will rank the rare synonymous variants according to their predicted harmfulness.

::DEVELOPER

Orion Buske and Michael Brudno

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Perl
  • Python
  • R package

:: DOWNLOAD

 SilVA

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Aug 1;29(15):1843-50. doi: 10.1093/bioinformatics/btt308.
Identification of deleterious synonymous variants in human genomes.
Buske OJ, Manickaraj A, Mital S, Ray PN, Brudno M.

sampletrees 20151127 / Rsampletrees 1.0.3 – Sampling Gene Genealogies Conditional on SNP Genotype data

sampletrees 20151127 / Rsampletrees 1.0.3

:: DESCRIPTION

The program sampletrees is a Markov chain Monte Carlo sampler of gene genealogies conditional on either phased or unphased SNP genotype data. The companion program Rsampletrees is for pre- and post-processing of sampletrees files, including setting up the files for sampletrees and storing and plotting the output of a sampletrees run.

::DEVELOPER

Graham & McNeney Labs

:: REQUIREMENTS

:: DOWNLOAD

 sampletrees / Rsampletrees 

:: MORE INFORMATION

Citation

sampletrees and Rsampletrees: Sampling gene genealogies conditional on SNP genotype data.
Burkett KM, McNeney B, Graham J.
Bioinformatics. 2016 Jan 18. pii: btv763.