Référentiel des outils installés sur la plateforme Migale
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
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.
Download : http://www.tree-puzzle.de/#download
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.
Documentation : http://genome.jouy.inra.fr/doc/genome/NGS/Trimmomatic-0.32/
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.
Documentation : http://genome.jouy.inra.fr/doc/genome/clustering/uclust/
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.
Download : http://www.drive5.com/usearch/download.html
Documentation : http://www.drive5.com/usearch/manual/
Usage : #usearch