A Sequence Viewer for basic bioinformatics. CLC Sequence Viewer creates a software environment enabling users to make a large number of bioinformatics analyses, combined with smooth data management, and excellent graphical viewing and output options. Remarque
|Run Unix # clcseqview6||Run Web #|
Debarcer (De-Barcoding and Error Correction) is a package for working with
next-gen sequencing data that contains molecular barcodes.
As it stands, it supports targeted sequencing libraries generated by
SimSenSeq, a method of creating multiplexed barcoded sequencing libraries
|Run Unix # runDebarcer.sh -u||Run Web #|
Within EMBOSS you will find around 100 programs (applications). These are just some of the areas covered (Sequence alignment, Rapid database searching with sequence patterns,Protein motif identification, including domain analysis, Nucleotide sequence pattern analysis, for example to identify CpG islands or repeats, Codon usage analysis for small genomes, Rapid identification of sequence patterns in large scale sequence sets, Presentation tools for publication...) Remarque
The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences (possibly with quality information). Remarque
The HH-suite is an open-source software package for highly sensitive sequence searching and sequence alignment. Its two most important programs are HHsearch and HHblits. Both are based on the pairwise comparison of profile hidden Markov models (HMMs).
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism.
JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish dump" command. See the documentation below for more details.Remarque If you use JELLYFISH in your research, please cite:
Guillaume Marcais and Carl Kingsford, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics (2011) 27(6): 764-770 (first published online January 7, 2011) doi:10.1093/bioinformatics/btr011
|Run Unix # jellyfish
||Run Web #|
The core of the LINKAGE package is a series of programs for maximum likelihood estimation of recombination rates, calculation of lod score tables, and analysis of genetic risks.Remarque linkmapslinkmap.tracesmakepedspreplinksilinkslodscoresmlink
|Run Unix # preplink ou linkmap ...||Run Web #|
Ce programme permet la détection de séquence d'ADN ribosomal 16S chimère (Une chimère correspond à la fusion de plusieurs séquences d'ADN r 16S). Remarque http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16957188&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum
|Run Unix # mallard||Run Web #|
NUPACK is a growing software suite for the analysis and design of nucleic acid systems. The package currently enables thermodynamic analysis of dilute solutions of interacting nucleic acid strands, and sequence design for complexes of nucleic acid strands intended to adopt a target secondary structure at equilibrium. NUPACK algorithms are formulated in terms of nucleic acid secondary structure. In most cases, pseudo-knots are excluded from the structural ensemble. Much of this software may be conveniently run through the NUPACK web server at http://www.nupack.org (Zadeh et al., 2010b). Remarque
PIPITS is an automated pipeline for analyses of fungal internal transcribed
spacer (ITS) sequences from the Illumina sequencing platform.
PIPITS is designed to work best on Bio-Linux
(http://environmentalomics.org/bio-linux/) and Ubuntu. Unfortunately, it's
NOT supported on Windows or a Mac
If you are using Bio-Linux, most of the dependencies are already on
Bio-Linux. Otherwise, you will have to set up the dependencies yourself. If
you are using Ubuntu, then instructions on how to set up dependencies are
described below (1.8).Remarque Citation
Hyun S. Gweon, Anna Oliver, Joanne Taylor, Tim Booth, Melanie Gibbs, Daniel S. Read, Robert I. Griffiths and Karsten Schonrogge, PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform, Methods in Ecology and Evolution, DOI: 10.1111/2041-210X.12399
|Run Unix # pipits_env||Run Web #|
This program takes a file containing DNA/RNA sequences in the FASTA format as input, and 1) makes prediction for putative mRNA polyadenylation sites [or poly(A) sites] and/or 2) generates results indicating the occurrences of different cis-elementRemarque
|Run Unix # polya_svm.pl ||Run Web #|
UCHIME is an algorithm for detecting chimeric sequences.
|Run Unix # uchime --input query.fasta [--db db.fasta] [--uchimeout results.uchime] [--uchimealns results.alns]
||Run Web #|
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. Remarque
|Run Unix # usearch
||Run Web #|
The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. RNA secondary structure prediction through energy minimization is the most used function in the package. We provide three kinds of dynamic programming algorithms for structure prediction: the minimum free energy algorithm of (Zuker & Stiegler 1981) which yields a single optimal structure, the partition function algorithm of (McCaskill 1990) which calculates base pair probabilities in the thermodynamic ensemble, and the suboptimal folding algorithm of (Wuchty et.al 1999) which generates all suboptimal structures within a given energy range of the optimal energy. For secondary structure comparison, the package contains several measures of distance (dissimilarities) using either string alignment or tree-editing (Shapiro & Zhang 1990). Finally, we provide an algorithm to design sequences with a predefined structure (inverse folding). Remarque