Référentiel des outils installés sur la plateforme Migale

La liste des packages R installés sur la plateforme Migale est disponible ici.

tmmod (version - 2009-02-23)
An Improved Hidden Markov Model for Transmembrane Protein Topology Prediction and Its Applications to Complete Genomes
Usage : #tmmod

tree-puzzle (version 5.2 - 2012-08-22)
TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. It implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. TREEPUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can be calculated with and without the molecular-clock assumption. In addition, TREE-PUZZLE o ers likelihood mapping, a method to investigate the support of a hypothesized internal branch without computing an overall tree and to visualize the phylogenetic content of a sequence alignment. TREE-PUZZLE also conducts a number of statistical tests on the data set (chi-square test for homogeneity of base composition, likelihood ratio to test the clock hypothesis, one and two-sided Kishino-Hasegawa test, Shimodaira-Hasegawa test, Expected Likelihood Weights). The models of substitution provided by TREE-PUZZLE are GTR, TN, HKY, F84, SH for nucleotides, Dayhoff, JTT, mtREV24, BLOSUM 62, VT, WAG for amino acids, and F81 for two-state data. Rate heterogeneity is modeled by a discrete Gamma distribution and by allowing invariable sites. The corresponding parameters (except for GTR) can be inferred from the data set.
Usage : #puzzle

Trimmomatic (version 0.32 - 2014-01-06)
Trimmomatic: A flexible read trimming tool for Illumina NGS dataTrimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.
Usage : #trimmomatic

uchime (version 4.2.40 - 2013-05-27)
UCHIME is an algorithm for detecting chimeric sequences.
Usage : #uchime --input query.fasta [--db db.fasta] [--uchimeout results.uchime] [--uchimealns results.alns]

uclust (version 1.2.22q - 2012-11-06)
UCLUST is a high-performance clustering, alignment and search algorithm that is capable of handling millions of sequences.
Usage : #uclust --sort seqs.fasta --output seqs_sorted.fasta

usearch (version 8.0.1517 - 2015-03-10)
USEARCH is a unique sequence analysis tool with thousands of users world-wide. USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST.
Usage : #usearch

VarScan (version 4.2.3 - 2017-02-16)
variant detection in massively parallel sequencing data???
Usage : #varscan [COMMAND] [OPTIONS]

Vcflib (version - 2017-03-10)
A C++ library for parsing and manipulating VCF files.

velvet (version 1.2.07 - 2013-08-07)
Sequence assembler for very short reads. Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
Usage : #velveth # velvetg

weeder (version 1.4.2 - 2009-12-07)
Recherche nouveaux TFBSs dans un jeu de sequences fasta, recherche de plusieurs tailles et limite de mutations autorisees. Ne sort que les motifs ayant passe le tri stat, contrairement a MEME qui donne autant de motifs que specifie dans les parametres. Par defaut les stat de genome sont basees sur un promoteur de 1000 pb, mais possibilite d'utiliser des stats basees sur toute la sequence intergenique.
Remarque : Pavesi G, Mereghetti P, Mauri G, Pesole G. Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes. Nucleic Acids Res. 2004 32:W199-W203
Usage : #weederlauncher.out inputfilename speciescode analysistype


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by Dr. Radut