Arrêt de l'ensemble des services de la plateforme Migale à partir du lundi 3 avril 2017

La plateforme Migale sera indisponible du 3 au 10 avril 2017. Cette indisponibilité est dûe à l'arrêt du DataCenter Ile-de-France qui héberge l'infrastructure de la plateforme.

Merci d'avance de votre compréhension.

Pour toutes questions ou informations supplémentaires, merci de contacter help.migale@jouy.inra.fr.

Divers


VersionMAJ

acnuc

none2003-08-09DownloadDoc
ACNUC allows to select sequences from many criteria from these three databases, to translate protein-coding genes in protein, and to extract selected sequences in user files. ACNUC is very efficient in providing direct access to coding regions (e.g. protein coding regions, tRNA or rRNA coding regions) of DNA fragments present in GenBank.

Remarque
Run Unix # acnuc ou pour la version X11 xacnucRun Web #

VersionMAJ

count_base

cc 30/06/20042004-06-16DownloadDoc
Programme pour compter les ATGC ds une sequence

Remarque
Run Unix # count_base.shRun Web #

VersionMAJ

count_codon

none2004-08-01DownloadDoc

Remarque
Run Unix # count_codon.plRun Web #

VersionMAJ

dsrc2

2.02016-10-17DownloadDoc
DNA Sequence Reads Compression is an application designed for compression of data files containing reads from DNA sequencing in FASTQ format. The amount of such files can be huge, e.g., a few (or tens) of gigabytes, so a need for a robust data compression tool is clear. Usually universal compression programs like gzip or bzip2 are used for this purpose, but it is obvious that a specialized tool can work better.

Remarque
Run Unix # usage: dsrc [options] Run Web #

VersionMAJ

fastPHASE

1.4.02015-03-10DownloadDoc
fastPHASE: software for haplotype reconstruction, and estimating missing genotypes from population data The program fastPHASE implements methods described in Scheet, P and Stephens, M (2006). A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet fastPHASE can handle larger data-sets than PHASE (e.g., hundreds of thousands of markers in thousands of individuals), but does not provide estimates of recombination rates. Our experiments suggest that haplotype estimates are slightly less accurate than from PHASE, but missing genotype estimates appear to be similar or even slightly better than PHASE.

Remarque
Run Unix # fastPHASE [options] Run Web #

VersionMAJ

ocount

0.42008-02-07DownloadDoc
OCOUNT is a fast C command-line utility that has been written in the course of TETRA's development. It counts oligonucleotides in DNA sequences and computes Markov-Model-based z-scores.

Remarque
Run Unix # ocountRun Web #

VersionMAJ

PROSE

DownloadDoc
The relational database PROSE contains protein sequences from Swissprot and Trembl

Remarque
Run Unix # Run Web # http://genome.jouy.inra.fr/prose

VersionMAJ

ratt

-2010-10-29DownloadDoc
RATT is software to transfer annotation from a reference (annotated) genome to an unannotated query genome.

Remarque
Run Unix # start.ratt.sh Run Web #

VersionMAJ

sequin

5.352005-07-01DownloadDoc
A DNA Sequence Submission and Update Tool

Remarque
Run Unix # sequinRun Web # http://www.ncbi.nlm.nih.gov/Sequin/

VersionMAJ

structure

2.3.42012-12-21DownloadDoc
The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.

Remarque
Run Unix # structureRun Web #

VersionMAJ

surf

1.02006-01-31DownloadDoc
SeqUence Repository and Feature detectionsNucleotidic sequence production commonly involve several dedicated bioinformatic softwares for sequence basecalling, vector detection, etc.

Remarque
Run Unix # Run Web #

VersionMAJ

wombat

23/02/112011-03-10DownloadDoc
WOMBAT is a program to facilitate analyses fitting a linear, mixed model via restricted maximum likelihood (REML). It is assumed that traits analysed are continuous and have a multivariate normal distribution.

Remarque http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2064953/ ~ http://didgeridoo.une.edu.au/km/download.php?file=hangzhou.pdf
Run Unix # wombatRun Web #

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