BLUP_GEN / BLUP_SNP – Estimate Solutions for Genomic Selection Models

BLUP_GEN / BLUP_SNP

:: DESCRIPTION

BLUP_GEN and BLUP_SNP are (Fortran90) programs to estimate solutions for genomic selection models, parameterized in terms of genomic relationship matrices or SNP effects. The programs accept heterogeneous variances as is often the case if pre-corrected phenotypes (DYD’s) are used

blup_snp computes solutions for snp effects considering them as random, with a common variance.

Blup_gen solves an equivalent system of equations based on G, the matrix of covariances among individuals.

::DEVELOPER

Andrés Legarra , andres dot legarra at toulouse point inra punto fr , Anne Ricard, Olivier Filangi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux
Fortran90

:: DOWNLOAD

BLUP_GEN / BLUP_SNP

:: MORE INFORMATION

PhyloMapper 1.0 beta 1 – Estimate Phylogeographic History using Genetic Data

PhyloMapper 1.0 beta 1

:: DESCRIPTION

PhyloMapper can be used to estimate phylogeographic history using genetic data. The statistical model implemented in PhyloMapper is unique in that it can be used as a descriptive tool and/or to test a priori hypotheses

::DEVELOPER

Lemmon Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ Linux / MacOsX
Java

:: DOWNLOAD

PhyloMapper

:: MORE INFORMATION

Citation

Syst Biol. 2008 Aug;57(4):544-61. doi: 10.1080/10635150802304761.
A likelihood framework for estimating phylogeographic history on a continuous landscape.
Lemmon AR, Lemmon EM.

BEBaC 20130425 – Estimate Bacterial Community Composition from 454 Sequencing data

BEBaC 20130425

:: DESCRIPTION

BEBaC (Bayesian Estimation of Bacterial Communities) is a software for estimating bacterial community composition from 454 sequencing data.

::DEVELOPER

Bayesian Statistics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
MUSCLE
Matlab

:: DOWNLOAD

BEBaC

:: MORE INFORMATION

Citation:

Lu Cheng, Alan W. Walker and Jukka Corander
Bayesian estimation of bacterial community composition from 454 sequencing data
Nucl. Acids Res. (2012) 40 (12): 5240-5249.

DEEGEP – Density Estimates by Expansions of GEgenbauer Polynomials

DEEGEP

:: DESCRIPTION

DEEGEP is a simple statistical method for testing for natural selection from a high dimensional (i.e. multiple population) allele frequency spectrum. The method uses a neutral control defined by the user (e.g. intergenic sites) to learn a background neutral distribution. This is accomplished by approximating the density with a finite expansion of Gegenbauer polynomials, inspired by Kimura’s classic result in theoretical population genetics. One can then test for natural selection on a second set of putatively functional sites (e.g. microRNAs) by comparing the multi-population allele frequency spectrum to the neutral control.

::DEVELOPER

Kevin Chen’s group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Mac OsX / Windows
Python

:: DOWNLOAD

DEEGEP

:: MORE INFORMATION

MDIV – Estimate Divergence Times and Migration Rates between two Populations

MDIV

:: DESCRIPTION

MDIV is a program that will simultaneously estimate divergence times and migration rates between two populations under the infinite sites model and under a finite sites model (HKY). The program can be used to test if there is evidence for migration between two populations or evidence for shared recent common ancestry. In addition, you get maximum likelihood estimates of the demographic parameters.

::DEVELOPER

the Nielsen group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows

:: DOWNLOAD

MDIV

:: MORE INFORMATION

Citation:

Genetics. 2001 Jun;158(2):885-96.
Distinguishing migration from isolation: a Markov chain Monte Carlo approach.
Nielsen R, Wakeley J.

PARENT-ASSIGN.XLS – Estimate minimal number of loci for Parentage Assignment

PARENT-ASSIGN.XLS

:: DESCRIPTION

PARENT-ASSIGN.XLS is an excell sheet to estimate minimal number of loci for parentage assignment.

:: DEVELOPER

Dr Louis Bernatchez

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / MacOsX
Excel

:: DOWNLOAD

PARENT-ASSIGN.XLS

:: MORE INFORMATION

CitationBERNATCHEZ, L., P. DUCHESNE. 2000.
Individual-based genotype analysis in studies of parentage and population assignment : how many loci, how many alleles ?
Canadian Journal of Fisheries and Aquatic Sciences. 57:1-12.

POP-ASSIGN.XLS – Estimate minimal number of loci for Population Assignment

POP-ASSIGN.XLS

:: DESCRIPTION

POP-ASSIGN.XLS is an Excell sheet to estimate minimal number of loci for Population Assignment

:: DEVELOPER

Dr Louis Bernatchez

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / MacOsX
Excel

:: DOWNLOAD

POP-ASSIGN.XLS

:: MORE INFORMATION

Citation

BERNATCHEZ, L., P. DUCHESNE. 2000.
Individual-based genotype analysis in studies of parentage and population assignment : how many loci, how many alleles ?
Canadian Journal of Fisheries and Aquatic Sciences. 57:1-12.

EPoS 0.91 – Estimating Phylogenies of Species

EPoS 0.91

:: DESCRIPTION

EPoS is a modular software framework for phylogenetic analysis and visualization. Existing phylogenetic software can be split into two groups. Algorithmic packages that provide computational methods for a specific problem, and visualization tools to analyse results. Many algorithmic tools lack in us ability, as they are often command line based, while visualizations often suffer from poor graphical user interfaces.

::DEVELOPER

Lehrstuhl Bioinformatik Jena

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / MacOsX

:: DOWNLOAD

EPoS

:: MORE INFORMATION

Citation:

EPoS: a modular software framework for phylogenetic analysis
Thasso Griebel; Malte Brinkmeyer; Sebastian Bocker
Bioinformatics , 24(20):2399-2400 2008; doi: 10.1093/bioinformatics/btn364

ContEst 1.0.24530 – Estimate Contamination Level in Sequencing data

ContEst 1.0.24530

:: DESCRIPTION

ContEst is a tool (and method) for estimating the amount of cross-sample contamination in next generation sequencing data. Using a Bayesian framework, contamination levels are estimated from array based genotypes and sequencing reads.

::DEVELOPER

The Cancer Genome Analysis (CGA) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac OsX / Windows
Java

:: DOWNLOAD

ContEst

:: MORE INFORMATION

Citation

Kristian Cibulskis, Aaron McKenna, Tim Fennel, Eric Banks, Mark DePristo and Gad Getz
ContEst: estimating cross-contamination of human samples in next-generation sequencing data
Bioinformatics (2011) 27 (18): 2601-2602.

GZ-gamma – Estimate Parameter of Substitution Rate Variation among Sites

GZ-gamma

:: DESCRIPTION

GZ-gamma is designed to estimate the expected number of substitutions of each amino acid (nucleotide) site, and the gamma shape parameter for the rate variation among sites, using a combination of ancestral sequence inference and maximum likelihood estimation when the phylogenetic relationships of these homologous sequences are known.

::DEVELOPER

Jianzhi Zhang , Xun Gu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows

:: DOWNLOAD

GZ-gamma

:: MORE INFORMATION

Citation:

Gu, X. and J. Zhang J (1997)
A simple method for estimating the parameter of substitution rate variation among sites.
Mol. Biol. Evol. 14:1106-1113