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.

Conversion de formats


VersionMAJ

fmtseq

1.2.22004-01-21DownloadDoc
Conversion de formats de sequence. Réimplémentation et extension du programme Readseq (conversion depuis et vers le format Clustalw et indication du format d'entrée.

Remarque Fait partie du paquetage seqio-1.2.2
Run Unix # fmtseqRun Web #

VersionMAJ

mktrace

0.001017 2005-07-30DownloadDoc
This program reads a FASTA file and creates a chromatogram stored in an SCF file and a corresponding phd file. The SCF file contains minimal information at this time. If a quality value FASTA file exists, mktrace uses those quality values in the phd file, otherwise it sets the quality values to the pre-determined values. mktrace produces a fake trace that could be used by Phred/Phrap packages.

Remarque Fait parti du package consed
Run Unix # mktrace G0771A003_114.s1.seq G0771A003_114.s1.scfRun Web #

VersionMAJ

mview

1.47.32003-05-16DownloadDoc
MView is a tool for converting the results of a sequence database search (BLAST, FASTA, etc.) into the form of a coloured multiple alignment of hits stacked against the query. Alternatively, an existing multiple alignment (MSF, PIR, CLUSTALW, etc.) can be processed. In either case, the output is simply HTML, so the result is platform independent and does not require a separate application or applet to be loaded. MView is NOT a multiple alignment program, nor is it a general purpose alignment editor.

Remarque
Run Unix # mview [options] [file...]Run Web #

VersionMAJ

phd2fasta

0.990622.f2005-07-22DownloadDoc
Phd2fasta reads phd files and writes sequence and quality value FASTA files, which phrap and cross_match need as input. Phred and consed write sequence and quality value information in 'phd' output files. A phd file contains information in a header, the called bases, the base quality values, and the base call trace locations.

Remarque
Run Unix # phd2fasta -id ../phd_dir -os fasta_seq -oq fasta_seq.qualRun Web #

VersionMAJ

readseq2

2.1.302014-06-23DownloadDoc
Read and reformat biosequences

Remarque
Run Unix # readseq2 [option]Run Web #

VersionMAJ

SAMtools

1.22015-04-15DownloadDoc
SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

Remarque
Run Unix # samtools [options]Run Web #

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