Référentiel des outils installés sur la plateforme Migale

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

newbler (version 2.6 - 2011-07-06)
Newbler is a package of three data analysis applications made by Roche 454 : the GS De Novo Assembler (with or without contig scaffolding using Paired End reads), the GS Reference Mapper, and the GS Amplicon Variant Analyzer (AVA). An additional application, the GS Run Browser, is an interactive Run browser/ troubleshooting tool which displays graphically the images, some intermediate data, and various output metrics from a sequencing Run. The software package also includes the SFF Tools commands for handling and using the data files (called Standard Flowgram Format or SFF files) that hold the sequencing trace data.
Usage : #newbler

NGSToolsMIG (version 1.0 - 2011-02-04)
Tools developed in MIG laboratory to help in the process of Next generation Sequencing Data analysis : quality control, mapping, assembly, global statistics, etc. ///////// adaptiveTrim.pl ///////// alignmentStatistics.pl ///////// contigsExtractionOnLength.pl ///////// fastqQualityConverter.pl ///////// gbk2Fasta.pl ///////// globalTrim.pl ///////// multiFasta2Fasta.pl ///////// show2Fasta.pl ///////// unmappedReadsExtraction.pl ///////// (Cf. Doc)
Usage : #ex.: contigsExtractionOnLength.pl -i fichier.fasta -do /Dir1/Dir11/Dir111/ -po fichierFiltre -l 1500 -r

njplot (version 2009 - 2013-08-27)
NJplot is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format (e.g., the format used by the PHYLIP package). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.
Usage : #njplot

novoalign (version 2.08.01 - 2013-08-20)
Novoalign is an aligner for single-ended and paired-end reads from the Illumina Genome Analyser. Novoalign finds global optimum alignments using full Needleman-Wunsch algorithm with affine gap penalties.
Usage : #novoalign [options]

paml (version 4.9 - 2015-03-30)
PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/Mac OSX, and executables are provided for MS Windows. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc.
Usage : ##baseml (basemlg codeml pamp evolver yn00 chi2)

pftools (version 2.3.4 - 2004-04-10)
Le paquetage pftools est une collection de programmes exp?rimentaux qui permet de manipuler le format g?n?ralis? de profils et impl?mente les m?thodes de recherche de PROSITE. Les commandes accessibles sont les suivantes : gtop, pfsearch, pfscan, psa2msa, pfmake, pfw, ptoh, htop, pfscale, pftof.
Usage : #pfsearch

PhageTerm (version - 2019-03-28)
Outil permettant d'identifier le mode d'empaquetage ds phages à partir de données de séquençage NGS The PhageTerm software is provided as a command line tool (https://sourceforge.net/projects/phageterm), as a Galaxy Toolshed, and on a Galaxy web server (https://galaxy.pasteur.fr).
Usage : #phageterm_env

Phobius (version 1.01 - 2018-05-23)
A combined transmembrane topology and signal peptide predictor
Usage : #phobius.pl [options] [infile]

phrap (version 1.090518 - 2010-01-18)
phrap is a program for assembling shotgun DNA sequence data. Among other features, it allows use of the entire read and not just the trimmed high quality part, it uses a combination of user-supplied and internally computed data quality information to improve assembly accuracy in the presence of repeats, it constructs the contig sequence as a mosaic of the highest quality read segments rather than a consensus, it provides extensive assembly information to assist in trouble-shooting assembly problems, and it handles large datasets.
Remarque : Marche avec cross_match et swat, loco et cluster La version manyreads permet de lire plus de trace.
Usage : #phrap

phred (version 020425.c - 2005-07-27)
Phred reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files. Phred can read trace data from chromatogram files in the SCF, ABI, and ESD formats. It automatically determines the file format, and whether the chromatogram file was compressed using gzip, bzip2, or UNIX compress. After calling bases, phred writes the sequences to files in either FASTA format, the format suitable for XBAP, PHD format, or the SCF format. Quality values for the bases are written to FASTA format files or PHD files, which can be used by the phrap sequence assembly program in order to increase the accuracy of the assembled sequence. phred, phrap, consed are Unix programs that work as a group for analysis of new DNA sequences. They do the following: phred: Base calling and quality assignments phrap: Contig formation and new quality assignments consed: Visual X-Windows graphic interface, to view and edit alignments and contigs, and to view the original traces
Usage : #phred ou phredPhrap


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by Dr. Radut