Référentiel des outils installés sur la plateforme Migale

mira (version 4.0 - 2014-11-18)
MIRA is a Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina. It can perform Hybrid de-novo assemblies as well as SNP and mutations discovery for mapping assemblies.
Usage : #mira

miranda (version 3.3a - 2014-10-29)
miRanda is an algorithm for the detection of potential microRNA target sites in genomic sequences. miRanda reads RNA sequences (such as microRNAs) from file1 and genomic DNA/RNA sequences from file2. Both of these files should be in FASTA format.
Usage : #miranda file1 file2 [options..]

modeller (version 9.16 - 2016-01-21)
MODELLER is used for homology or comparative modeling of protein three-dimensional structures (1,2). The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms.
Usage : #usage: mod9.16 script [...]

MOSAIK assembler (version 1.1.0021 - 2011-06-06)
MOSAIK is a reference-guided assembler comprising of four main modular programs: * MosaikBuild * MosaikAligner * MosaikSort * MosaikAssembler. MosaikBuild converts various sequence formats into Mosaik’s native read format. MosaikAligner pairwise aligns each read to a specified series of reference sequences. MosaikSort resolves paired-end reads and sorts the alignments by the reference sequence coordinates. Finally, MosaikAssembler parses the sorted alignment archive and produces a multiple sequence alignment which is then saved into an assembly file format.
Usage : #MosaikAligner MosaikAssembler MosaikBuild MosaikCoverage MosaikDupSnoop MosaikJump MosaikMerge MosaikSort MosaikText

mothur (version 1.34,4 - 2014-12-23)
The goal of mothur is to have a single resource to analyze molecular data that is used by microbial ecologists. Many of these tools are available elsewhere as individual programs and as scripts, which tend to be slow or as web utilities, which limit your ability to analyze your data. mothur offers the ability to go from raw sequences to the generation of visualization tools to describe α and β diversity. Examples of each command are provided within their specific pages, but several users have provided several analysis examples, which use these commands. An exhaustive list of the commands found in mothur is available within the commands category index.
Usage : #mothur

MrBayes (version 3.2.5 - 2015-10-20)
MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.
Usage : #mb

MuGeN (version 20060919 - 2007-01-05)
MuGeN (Multi-Genome Navigator) est un outil interactif permettant une exploration dans plusieurs géomes annotés complets par des résultats d'analyse in silico. Il dispose également d'un mode d'exécution en mode batch lui permettant de servir de générateur d'images à divers formats. Ce mode de fonctionnement le prédispose à être intégré à des sites Web pour l'affichage de cartes physiques annotées. MuGeN is a software package for the visual exploration of multiple annotated genome portions. It is capable of simultaneously displaying genome portions loaded from various sources both local and remote and mix these with analysis result plots. It can also be used to generate images of these displays in a wide range of formats (PNG, PostScript, IMAP, XFig).
Remarque : La commande : mugenv est suffisante pour lancer l'environnement graphique, mais elle ne charge aucun genome et les fenêtres paraîtront donc un peu vides. Plus fréquemment, on fera : mugenv /chemin/vers/un/fichier/genbank.gbk pour explorer le fichier en question. Les numéros de version de MuGeN correspondent à leur date de sortie, et sont affichées dans la barre titre de sa fenêtre graphique. La derniére en date est la 20040726 qui est celle installée sur topaze et adm.
Usage : #mugenv ou mugenv /chemin/vers/un/fichier/genbank.gbk

mummer (version 3.23 - 2015-03-02)
MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences.
Usage : #mummer [options]

muscle (version 3.8.31 - 2014-08-24)
MUSCLE stands for MUltiple Sequence Comparison by Log-Expectation.
Usage : #muscle -in -out

NCBi Blast + (version 2.6.0 - 2017-08-22)
BLAST+ is a suite of command-line tools to run BLAST


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by Dr. Radut