Varclus – Detection of Positive Selection in Genes and Genomes through Variation Clusters

Varclus

:: DESCRIPTION

Varclus is a perl utility to identify clusters of amino acid or nucleotide changes in a sequence that are too tightly spaced to have occurred by chance alone.

::DEVELOPER

Andreas Wagner Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Perl

:: DOWNLOAD

 Varclus

:: MORE INFORMATION

Citation:

Wagner, A. (2007)
Rapid detection of positive selection in genes and genomes through variation clusters.
Genetics 176: 2451–2463

SCCT – Dectect Recent Positive Selection by Conditional Coalescent Tree

SCCT

:: DESCRIPTION

SCCT (Selection detection by Conditional Coalescent Tree) is a efficiency computational software developed to detect recent positive selection using deep sequencing data. It’s robust to various demographic events and also robust to the variations of mutation rates and recombination rates.

::DEVELOPER

SCCT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java
  • Python

:: DOWNLOAD

  SCCT

:: MORE INFORMATION

Citation:

Detecting recent positive selection with high accuracy and reliability by conditional coalescent tree.
Wang M, Huang X, Li R, Xu H, Jin L, He Y.
Mol Biol Evol. 2014 Nov;31(11):3068-80. doi: 10.1093/molbev/msu244.

MFDM 1.1 – Detect recent Positive Selection Reliably in Natural Populations

MFDM 1.1

:: DESCRIPTION

MFDM (Maximum Frequency of Derived Mutations) is designed to reliably detect recent positive selection in a varying size population, even if you only have polymorphism data from a single locus (i.e. a very short piece of DNA).

::DEVELOPER

Evolutionary Genomics Lab, PICB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Java

:: DOWNLOAD

 MFDM

:: MORE INFORMATION

Citation

A new test for detecting recent positive selection that is free from the confounding impacts of demography.
Li H.
Mol Biol Evol. 2011 Jan;28(1):365-75. doi: 10.1093/molbev/msq211.

selscan 1.3.0 – EHH-based Scans for Positive Selection

selscan 1.3.0

:: DESCRIPTION

selscan is a program to calculate EHH-based scans for positive selection in genomes

::DEVELOPER

SZPIECH LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

 selscan

:: MORE INFORMATION

Citation

Mol Biol Evol. 2014 Oct;31(10):2824-7. doi: 10.1093/molbev/msu211. Epub 2014 Jul 10.
selscan: an efficient multithreaded program to perform EHH-based scans for positive selection.
Szpiech ZA, Hernandez RD

Haplotter – Explore the Evidence for Recent Positive Selection in the Human Genome

Haplotter

:: DESCRIPTION

Haplotter is a web application that has been developed to display the results of a scan for positive selection in the human genome using the HapMap data.

::DEVELOPER

Pritchard Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS Biol. 2006 Mar;4(3):e72. Epub 2006 Mar 7.
A map of recent positive selection in the human genome.
Voight BF1, Kudaravalli S, Wen X, Pritchard JK.

FastCodeML 1.1.0 – Fast Detection of Positive Selection on Phylogenetic Trees

FastCodeML 1.1.0

:: DESCRIPTION

FastCodeML is a software to infer positive selection along positions of a protein coding gene using the Branch-Site model of evolution (Yang and Nielsen, 2002, Mol Biol Evol).

::DEVELOPER

The Computational Phylogenetics group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FastCodeML

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jan 23.
Optimization strategies for fast detection of positive selection on phylogenetic trees.
Valle M1, Schabauer H, Pacher C, Stockinger H, Stamatakis A, Robinson-Rechavi M, Salamin N.

PoSeiDon – Positive Selection Detection and Recombination Analysis

PoSeiDon

:: DESCRIPTION

PoSeiDon is a pipeline to detect significant positively selected sites and possible recombination events in analignment of multiple coding sequences. Sites that undergo positive selection can give you insights in the evolutionary history of your sequences, for example showing you important mutation hot spots, accumulated as results of virus-host arms races during evolution.

::DEVELOPER

RNA Bioinformatics and High Throughput Analysis Jena

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 PoSeiDon

:: MORE INFORMATION

Optimist 20130226 – Inference of Positive Selection

Optimist 20130226

:: DESCRIPTION

Optimist is a simple software package for inferring positive selection from marker dynamics in an asexual population.

::DEVELOPER

Chris Illingworth.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C Compiler

:: DOWNLOAD

 Optimist

:: MORE INFORMATION

Citation

A method to infer positive selection from marker dynamics in an asexual population.
Illingworth CJ and Mustonen V
Bioinformatics (Oxford, England) 2012;28;6;831-7

InVEx – Ascertain Genes with a Somatic Mutation Distribution showing evidence of Positive Selection for non-silent Mutations

InVEx

:: DESCRIPTION

InVEx (Introns Vs Exons) is a permutation-based method for ascertaining genes with a somatic mutation distribution showing evidence of positive selection for non-silent mutations. The method was developed for use in cancer genomics studies, with particular relevance to high mutation rate cancers. Mutations are permuted on a per-patient, per-trinucleotide-context basis across the exons, introns and UTRs of a gene, generating a null model of the distribution of mutations to which the observed distribution can be compared to determine statistical significance. Significant genes are of interest, as their somatic mutation is likely to be important in the formation of the cancer being studied. The method can operate on whole exome as well as whole genome sequencing data.

::DEVELOPER

Broad Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Python
  • R package

:: DOWNLOAD

 InVEx

:: MORE INFORMATION

Citation:

Hodis and Watson et al
A Landscape of Driver Mutations in Melanoma
Cell, Volume 150, Issue 2, 251-263, 20 July 2012

MCMCcodonsite – Identify Sites under Positive Selection

MCMCcodonsite

:: DESCRIPTION

 MCMCcodonsite is a program implementing some codon models allowing \omega = d_N/d_S to vary among sites (M0, M2a, M3, M7, M8) in a Bayesian framework

::DEVELOPER

The Aris-Brosou lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • PAML

:: DOWNLOAD

 MCMCcodonsite

:: MORE INFORMATION

Citaion

Aris-Brosou, S. 2006.
Identifying sites under positive selection with uncertain parameter estimates.
Genome. 49:767-776.