Référentiel des outils installés sur la plateforme Migale
La liste des packages R installés sur la plateforme Migale est disponible ici.
StringTie (version 1.3.0 - 2016-09-07)
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-lengthtranscripts representing multiple splice variants for each gene locus. Itsinput can include not only the alignments of raw reads used by othertranscript assemblers, but also alignments longer sequences that have beenassembled from those reads.In order to identify differentially expressedgenes between experiments, StringTie's output can be processed by specialized software like Ballgown, Cuffdiff or other programs (DESeq2, edgeR, etc.).
Documentation : https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual
Usage : #stringtie -h/--help
structure (version 2.3.4 - 2012-12-21)
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.
Download : http://pritch.bsd.uchicago.edu/structure_software/release_versions/v2.3.4/html/structure.html
Usage : #structure
SUPER-FOCUS (version 0.26 - 2016-10-04)
SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agilehomology-based approach using a reduced SEED database to report thesubsystems present in metagenomic samples and profile their abundances. Thetool was tested with over 70 real metagenomes, and the results show that ourapproach accurately predicts the subsystems present in microbial communities,and it can be up to over 1,000 times faster than other tools.
surf (version 1.0 - 2006-01-31)
SeqUence Repository and Feature detectionsNucleotidic sequence production commonly involve several dedicated bioinformatic softwares for sequence basecalling, vector detection, etc.
Documentation : http://genome.jouy.inra.fr/doc/genome/edition/surf-1.0/
SurfG+ (version 1.02 - 2012-07-13)
SurfG+ is a tool to predict the protein localization in frame-psoitive bacteria. Current protein localization protocols are not suited to this prediction task as they ignore the potential surface exposition of many membrane-associated proteins. Therefore, we developed a new flow scheme, for the processing of protein sequence data with the particular aim of identification of potentially surface exposed (PSE) proteins from Gram-positive bacteria.
Remarque : See Barinov A, Loux V, Hammani A, Nicolas P, Langella P, Ehrlich D, et al. Prediction of surface exposed proteins in Streptococcus pyogenes, with a potential application to other Gram-positive bacteria.Proteomics. 2009 Jan.;9(1):61–73.
Usage : #Surfg
tablet (version 220.127.116.11 - 2015-04-07)
Tablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments.
Documentation : http://bioinf.scri.ac.uk/tablet/index.shtml
Usage : #tablet
Tandem Repeats Finder (version 4.07b - 2013-08-20)
A tandem repeat in DNA is two or more adjacent, approximate copies of a pattern of nucleotides. Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences.
Download : http://tandem.bu.edu/trf/trf.download.html
Documentation : http://tandem.bu.edu/trf/trf.unix.help.html
Usage : #trf
T-Coffee (version 11.00.8cbe486 - 2015-04-07)
T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Version 2.00 and higher can mix sequences and structures.
Documentation : http://www.tcoffee.org/Projects/tcoffee/#DOCUMENTATION
Usage : #t_coffee sequence_file
TFM-Pvalue (version - - 2014-01-14)
TFM-Pvalue is a software suite providing tools for computing the score threshold associated to a given P-value and the P-value associated to a given score threshold. It uses Position Weight Matrices, such as those available in the Transfac or Jaspar databases.
Remarque : Efficient and accurate P-value computation for Position Weight MatricesH. Touzet and J.S. VarréAlgorithms for Molecular Biology 2007, 2:15
tmhmm (version 2.0c - 2007-11-22)
tmhmm is one of the better prediction methods of transmembrane helices in proteinss
Documentation : http://www.cbs.dtu.dk/services/TMHMM/TMHMM2.0b.guide.php
Remarque : tmhmm ma_sequence.fasta puis le resultat est genere sur la sortie standard (pas tres bavard) et dans un repertoire nomme TMHMM_
avec etant le PID du processus qui l a genere.
Usage : #tmhmm