Multilocus 1.3b – Analysis of Multi-locus Population Genetic Data

Multilocus 1.3b

:: DESCRIPTION

Multilocus has been written to facilitate analysis of multi-locus population genetic data. In particular, it allows calculation of various genotypic diversity indices, various linkage disequilibrium indices, and a measure of population differentiation, and allows one to search for subpopulations which do not share polymorphisms (and thus might be reproductively isolated). It includes a modification of the IA (Index of Association) metric that corrects the scaling effect seen when one applies the metric to different numbers of loci. In addition, there are randomization routines which allow one to test various null hypotheses.

::DEVELOPER

Paul-Michael Agapow and Austin Burt (a.burt@imperial.ac.uk), Dept. Biology, University College London

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX

:: DOWNLOAD

 Multilocus

:: MORE INFORMATION

NNPERM 1.3 – Analyse Case-control Multi-locus Genotype Data

NNPERM 1.3

:: DESCRIPTION

NNPERM is a neural network program for analysing case-control multi-locus genotype data using a permutation test.

::DEVELOPER

Bernard North

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

NNPERM

:: MORE INFORMATION

Citation:

B.V. North, D. Curtis, P.G.Cassell, G.A.Hitman and P. C. Sham
Assessing optimal neural network architecture for identifying disease-associated multi-marker genotypes using a permutation test, and application to calpain 10 polymorphisms associated with diabetes.
Annals of Human Genetics 67: 348-356

msABC 20120315 – Modification of Hudson’s ms to facilitate Multi-locus ABC analysis

msABC 20120315

:: DESCRIPTION

msABC is a program for simulating various neutral evolutionary demographic scenarios based on the software ms (Hudson 2002). msABC extends ms, calculating a multitude of summary statistics. Therefore, msABC is suitable for performing the sampling step of an Approximate Bayesian Computation analysis (ABC), under various neutral demographic models.

::DEVELOPER

Pavlos Pavlidis

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler
  • R package

:: DOWNLOAD

 msABC

:: MORE INFORMATION

Citation:

Mol Ecol Resour. 2010 Jul;10(4):723-7. doi: 10.1111/j.1755-0998.2010.02832.x. Epub 2010 Feb 2.
msABC: a modification of Hudson’s ms to facilitate multi-locus ABC analysis.
Pavlidis P, Laurent S, Stephan W.

mlgt 0.16 – Multi-Locus Geno-Typing

mlgt 0.16

:: DESCRIPTION

mlgt is an R package for processing and analysis of high throughput (Roche 454) sequences generated from multiple loci and multiple biological samples. Sequences are assigned to their locus and sample of origin, aligned and trimmed. Where possible, genotypes are called and variants mapped to known alleles.

::DEVELOPER

Dave Gerrard

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/MacOsX
  • R package

:: DOWNLOAD

 mlgt

:: MORE INFORMATION

SUMSTAT / SumstatQ – Sum Statistics for multi-locus Genetic Association Mapping

SUMSTAT / SumstatQ

:: DESCRIPTION

SUMSTAT considers a number of marker loci in the genome. At each marker, genotypes are available for two types of observations

sumstatQ represents a modification of the sumstat program in that it works with quantitative phenotypes (QTLs) rather than case-control type data. The datafile structure is the same as for sumstat but after the input lines containing genotype data, one or more QTLs can be present, one per input line for each individual.

::DEVELOPER

Jurg Ott, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 SUMSTAT / SumstatQ 

:: MORE INFORMATION

Citation

Ott J, Hoh J (2012)
Scan statistics in human gene mapping.
Am J Hum Genet 91, 970 (letter)

SHARE 1.1.0 – Multi-locus Analysis

SHARE 1.1.0

:: DESCRIPTION

SHARE (SNP-Haplotype Adaptive Regression) is an R code to perform multi-locus analysis in order to account for LD patterns observed in human genome.

::DEVELOPER

James Dai (jdai@scharp.org) ,Charles Kooperberg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SHARE 

:: MORE INFORMATION

Citation

James Y. Dai and Michael Leblanc
SHARE: an adaptive algorithm to select the most informative set of SNPs for candidate genetic association
Biostatistics. 2009 October; 10(4): 680–693.

Wright_Fisher_MP / Moran_MP – Multi-locus Match Probability

Wright_Fisher_MP / Moran_MP

:: DESCRIPTION

Wright_Fisher_MP and Moran_MP computes the multi-locus match probability (ie. the joint probability of identity by descent) between two haplotypes sampled without replacement from a finite population evolving under the Wright-Fisher and Moran models

::DEVELOPER

Anand Bhaskar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Wright_Fisher_MP and Moran_MP

:: MORE INFORMATION

Citation

Multi-locus match probability in a finite population: A fundamental difference between the Moran and Wright-Fisher models.
Bhaskar, A. and Song, Y.S.
Bioinformatics, 25 (2009) i187-i195.