ClonalFrame 1.2 / ClonalFrameML 1.0 – Inference of Bacterial Microevolution using Multilocus Sequence data

ClonalFrame 1.2 / ClonalFrameML 1.0

:: DESCRIPTION

ClonalFrame is a computer package for the inference of bacterial microevolution using multilocus sequence data.In a nutshell, ClonalFrame identifies the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance.ClonalFrame can be applied to any kind of sequence data, from a single fragment of DNA to whole genomes. It is well suited for the analysis of MLST data, where 7 gene fragments have been sequenced, but becomes progressively more powerful as the sequenced regions increase in length and number up to whole genomes. However, it requires the sequences to be aligned. If you have genomic data that is not aligned, we recommend using Mauve which produces alignment of whole bacterial genomes in exactly the format required for analysis with ClonalFrame.

ClonalFrameML is a software package that performs efficient inference of recombination in bacterial genomes.

::DEVELOPER

Xavier Didelot and Daniel Wilson

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

 ClonalFrame , ClonalFrameML

:: MORE INFORMATION

Citation

ClonalFrameML: efficient inference of recombination in whole bacterial genomes.
Didelot X, Wilson DJ.
PLoS Comput Biol. 2015 Feb 12;11(2):e1004041. doi: 10.1371/journal.pcbi.1004041.

Didelot and Falush (2007)
Inference of Bacterial Microevolution Using Multilocus Sequence Data
Genetics March 2007 vol. 175 no. 3 1251-1266

COLONY 20150217 – Parentage and Sibship Inference from Multilocus Genotype data

COLONY 20150217

:: DESCRIPTION

COLONY is a Fortran program that implements a maximum likelihood method to assign sibship and parentage jointly, using individual multilocus genotypes at a number of codominant or dominant marker loci.

:: DEVELOPER

Dr Jinliang Wang

:: SCREENSHOTS

COLONY

:: REQUIREMENTS

  • Windows / MacOsX

:: DOWNLOAD

 COLONY

:: MORE INFORMATION

Citation

Jones, O. and Wang, J. (2009)
COLONY: a program for parentage and sibship inference from multilocus genotype data.
Molecular Ecology Resources 10: 551–555.

Wang, J. (2012)
Computationally efficient sibship and parentage assignment from multilocus marker data.
Genetics 191: 183-194.

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

HAPSIM – Produce the Case-control Multilocus Genotype Data

HAPSIM

:: DESCRIPTION

HAPSIM is a program for generating case-control multi-locus genotype data under a specified disease model.

::DEVELOPER

Bernard North

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

HAPSIM

:: 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

LIAN 3.7 – Testing Genome-Wide Linkage Equilibrium From Multilocus Data

LIAN 3.7

:: DESCRIPTION

LIAN is a program to test the null hypothesis of linkage equilibrium for multilocus data.

::DEVELOPER

Bernhard Haubold

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 LIAN

:: MORE INFORMATION

Citation

Bioinformatics. 2000 Sep;16(9):847-8.
LIAN 3.0: detecting linkage disequilibrium in multilocus data. Linkage Analysis.
Haubold B1, Hudson RR.

Gencount 1.0 – Counts the Number of different Multilocus Genotypes

Gencount 1.0

:: DESCRIPTION

The Gencount reads a data file with L loci and counts the number of different multilocus genotypes for all possible sub-matrixes with l loci (l from 1 to L).

::DEVELOPER

Marine Ecology and Evolution :: MAREE

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Gencount

:: MORE INFORMATION

Cri-Map 2.4 – Construct Multilocus Linkage Map

Cri-Map 2.4

:: DESCRIPTION

CRI-MAP‘s purpose is to allow rapid, largely automated construction of multilocus linkage maps (and facilitate the attendant tasks of assessing support relative to alternative locus orders, generating LOD tables, and detecting data errors). Although originally designed to handle codominant loci (e.g. RFLPs) scored on pedigrees “without missing individuals”, such as CEPH or nuclear families, it can now (with some caveats described below) be used on general pedigrees, and some disease loci.

::DEVELOPER

Matise Laboratory of Computational Genetics.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows wity Cygwin /MacOsX
  • GCC
:: DOWNLOAD

  CRI-MAP

:: MORE INFORMATION

Citation

Hum Hered. 1995 Mar-Apr;45(2):103-16.
Parallel computation of genetic likelihoods using CRI-MAP, PVM, and a network of distributed workstations.
Matise TC, Schroeder MD, Chiarulli DM, Weeks DE.