SECA – Perform SNP Effect Concordance Analysis using Genome-wide Association Summary

SECA

:: DESCRIPTION

SECA (SNP Effect Concordance Analysis) is a user-friendly web-based application to perform SNP effect concordance analysis using GWA summary results.

::DEVELOPER

the Statistical and Genomic Epidemiology Laboratory (SGEL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 SECA

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 17. [Epub ahead of print]
SECA: SNP effect concordance analysis using genome-wide association summary results.
Nyholt DR.

BUCKy 1.4.4 – Gene Tree Reconciliation with Bayesian Concordance Analysis

BUCKy 1.4.4

:: DESCRIPTION

BUCKy (Bayesian Untangling of Concordance Knots) is a free program that implements Bayesian concordance analysis. The method uses a non-parametric clustering of genes with compatible trees, and reconstructs the primary concordance tree from clades supported by the largest proportions of genes. A population tree with branch lengths in coalescent units is estimated from quartet concordance factors. BUCKy estimates the dominant history of sampled individuals, and how much of the genome supports each relationship, using Bayesian concordance analysis. BUCKy does not assume that genes (or loci) all have the same topology. Instead, groups of genes sharing the same tree are detected (while accounting for uncertainty in gene tree estimates), and then combined to gain more resolution on their common tree. No assumption is made regarding the reason for discordance among gene trees.

::DEVELOPER

Cécile Ané Bret Larget

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • C++ Compiler

:: DOWNLOAD

BUCKy

:: MORE INFORMATION

Citation

B. Larget, S.K. Kotha, C.N. Dewey, C. Ané (2010).
BUCKy: Gene tree / species tree reconciliation with the Bayesian concordance analysis.
Bioinformatics (2010) September 21, 2010 doi: 10.1093/bioinformatics/btq539