Cartographie et Analyse génétique


VersionMAJ

carthagene

1.22010-10-15DownloadDoc
CarthaGène is a genetic/radiated hybrid mapping software. CarthaGene looks for multiple populations maximum likelihood consensus maps using a fast EM algorithm for maximum likelihood estimation and powerful ordering algorithms. CarthaGène:

Remarque
Run Unix # carthageneRun Web #

VersionMAJ

dadi

1.72016-07-18DownloadDoc
Diffusion Approximation for Demographic Inference ∂a∂i implements methods for demographic history and selection inference from genetic data, based on diffusion approximations to the allele frequency spectrum. One of ∂a∂i's main benefits is speed: fitting a two-population model typically takes around 10 minutes, and run time is independent of the number of SNPs in your data set. ∂a∂i is also flexible, handling up to three simultaneous populations, with arbitrary timecourses for population size and migration, plus the possibility of admixture and population-specific selection.

Remarque If you use ∂a∂i in your research, please cite RN Gutenkunst, RD Hernandez, SH Williamson, CD Bustamante "Inferring the joint demographic history of multiple populations from multidimensional SNP data" PLoS Genetics 5:e1000695 (2009).
Run Unix # Run Web #

VersionMAJ

fpc

8.92007-11-13DownloadDoc
FPC (fingerprinted contigs) is an interactive program for building contigs from fingerprinted clones, where the fingerprint for a clone is a set of restriction fragments.

Remarque
Run Unix # fpcRun Web #

VersionMAJ

mega2

4.5.62012-08-06DownloadDoc
Mega2 est un logiciel qui sert à partir de trois fichiers d'entrée (pedigree, carte et locus) à créer tous les fichiers nécessaires à l'utilisation de logiciels d'analyse de liaison, d'haplotypes, d'IBD etc.. comme simwalk2, genehunter, vitesse, TDT, SAGE, Allegro ou encore Mendel. Sans Mega2, il faut formater tous les input ce qui est long, fastidieux et source d'erreurs...

Remarque If you use Mega2 as part of a published work, please remember to reference Mega2. You may reference it by citing the following: Mukhopadhyay N, Almasy L, Schroeder M, Mulvihill WP, Weeks DE (2005) Mega2: data-handling for facilitating genetic linkage and association analyses. Bioinformatics. 2005 May 15;21(10):2556-7. PMID: 15746282
Run Unix # mega2Run Web #

VersionMAJ

merlin

1.1.22008-10-15DownloadDoc
MERLIN est un package qui permet d'effectuer des analyses génétiques rapides de pedigrees (analyses de liaison, d'association, haplotypes...).

Remarque
Run Unix # merlinRun Web #

VersionMAJ

plink

1.902015-02-24DownloadDoc
PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

Remarque For documentation, citation & bug-report instructions: http://pngu.mgh.harvard.edu/purcell/plink/
Run Unix # plinkRun Web #

VersionMAJ

SimWalk2

2.912007-01-31DownloadDoc
SimWalk2 is a statistical genetics computer application for haplotype, parametric linkage, non-parametric linkage (NPL), identity by descent (IBD) and mistyping analyses on any size of pedigree. SimWalk2 uses Markov chain Monte Carlo (MCMC) and simulated annealing algorithms to perform these multipoint analyses.

Remarque Ces fichiers sont indispensables a l'utilisation de SimWalk2 et doivent être là où on lancera le soft. (MAP.DAT, LOCUS.DAT, PEDIGREE.DAT, PEN.DAT).
Run Unix # simwalk2Run Web #

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