• Generic tools
  
• Sequencing and cartography
  
• Alignments and sequence comparison
  
• Phylogeny and comparative genomics
  
• Annotation
  
• Pattern search
  
• DNA sequences
  
• RNA sequences
  
• Proteic analysis
  
• Sequence format conversion
  

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Generic tools

	Name	Description	Link
	ACNUC	Retrieval system for the nucleotide sequence databases GenBank or EMBL and for the protein sequence databases SWISS-PROT or NBRF.	ACNUC webpage
	DS GCG	Commercial open source software package for sequence analysis.	Accelrys website
	EMBOSS at Pasteur Paris	European Molecular Biology Open Software Suite	Online forms
	EMBOSS in Bordeaux		online forms
	EMBOSS in Lille	European Molecular Biology Open Software Suite	online forms
	EMBOSS in Strasbourg	European Molecular Biology Open Software Suite	online forms
	EMBOSS in Toulouse	European Molecular Biology Open Software Suite	EMBOSS GUI
	FamFetch	the general interface used to query the families databases developed using the HOBACGEN model	FamFetch webpage
	Figenix	automates complex pipelines of phylogenetic analysis, gene prediction and EST analysis under the supervision of an expert system	Figenix server
	GOLDEN	A tool to search the nucleic and proteic databases.	webpage
	Mobyle	Mobyle is a framework and web portal specifically aimed at the integration of bioinformatics software and databanks	Mobyle web portal
	Remora	workflow generator and launcher, repository of predefined workflows and survey system	Remora’s server

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Sequencing and cartography

	Name	Description	Link
	AGMIAL	an integrated system for bacterial genome annotation.	webpage
	BioMercator	graphical map browser which performs automatic compilations of several genetic maps and computes meta-analysis of QTLs	Homepage
	CAP CAP2 CAP3	Contig assembly program	cap3 home
	Cassis	methods for precise detection of genomic rearrangement breakpoints	Download Cassis
	Consed	viewing, editing, and finishing sequence assemblies created with phrap	Consed webpage
	CRH_server	Comparative and Radiation Hybrid Server for the Canine Genome	Server homepage
	ISLAND	Program to simulate the progress of an STS mapping project	webpage
	MCQTL	A software application for QTL (Quantitative Trait Loci) mapping in multi-cross design.	webpage
	MuGeN	a software package for the visual exploration of multiple annotated genome portions.	webpage
	Phrap	a program for assembling shotgun DNA sequence data	webpage

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Alignments and sequence comparison

	Name	Description	Link
	16S rDNA Bacterial Identification	16S bacterial cultures Blast Server	Blast on sequences from cultured bacteria
	Automat	retrieve sequences distantly related to the query	Automat online
	Ballast	Blast results post-processing program extracting as much information as possible from stacked BlastP HSPs to help the interpretation of Blast results and the characterization of the query sequence	online forms
	BIBI	Bio Informatic Bacterial Identification	homepage
	BLAST	Basic Local Alignment Search Tool
	ClustalW and X	A general purpose multiple sequence alignment program for DNA or proteins.
	Clustering : Secator/DPC	Secator : a program for inferring protein subfamilies from phylogenetic trees - DPC : Density of points clustering, application to transcriptomics data analysis.	online form
	COMBAT	COMBined AlignmenT - Comparison of coding DNA	online form
	COSA	Clustal ouput structural analysis	online form
	DbClustal	global multiple alignments of protein sequences detected by database searches	online form
	DbW	Automatic update of a functional family-specific multiple alignment	webpage
	ESPript	a tool whose output is a PostScript file of aligned sequences with graphical enhancements. The program calculates a similarity score for each residue of the aligned sequences.	more information
	FASTA	Provides sequence similarity searching against nucleotide and protein databases.
	HMMer	an implementation of profile hidden Markov model (HMM) methods for sensitive database searches using multiple sequence alignments as queries	more information
	IMGT/V-QUEST	Sequence alignment of immunoglobulin and T cell receptor variable genes	online form
	Lalnview	a graphical program for visualizing local alignments between two sequences (protein or nucleic acids)	homepage
	LEON	multiple aLignment Evaluation Of Neighbours	online form
	MOSAIC	a relational database and web interface developed to compare closely related bacterial genomes	Mosaic online
	Multalin	multiple alignment with hierarchical clustering	online form
	MUMmer	rapidly aligning entire genomes	MUMmer homepage
	Mview	visualization of alignments and conversion into different formats (MSF, clustalw, Pearson Fasta, Pir, ...)	online form at Pasteur Paris
	NorMD	objective scoring function for protein multiple sequence alignments
	PipeAlign	on-line protein family analysis tool providing both interactive and automatic workbench for the validation, integration and presentation	online form
	Rascal	Rapid scanning and correction of multiple sequence alignment programs.	online form
	SeaView	graphical multiple sequence alignment editor	homepage
	SIM4	efficiently aligning a transcribed and spliced DNA sequence (mRNA, EST) with a genomic sequence containing that gene	online form
	Tcoffee	A web server for mixing Sequences and Structures into multiple sequence alignments	homepage
	vALId	Validation of protein sequence quality based on multiple ALIgnment data	homepage
	WISE	Comparison of a protein and a DNA sequence (genomic or cDNA)	online form

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Phylogeny and comparative genomics

	Name	Description	Link
	ape	R-package for Analyses of Phylogenetics and Evolution	CRAN - package ape
	AthGInRel	Allows to penetrate inside the Arabidopsis genome for studying the inter-relation which exist for each genes (duplication alone, multigenic family).	software info
	BAOBAB	editor for large phylogenetic trees	homepage
	BCG	bacterian genomic comparative tools	BCG online
	BioNJ	a version of the NJ algorithm improved for molecular sequences	online form
	Cassis	methods for precise detection of genomic rearrangement breakpoints	Download Cassis
	dnadist	Program to compute distance matrix from nucleotide sequences	online form
	dnapars	DNA Parsimony Program	online form
	DT-SCORE	a distance based tandem duplication tree reconstruction algorithm.	webpage
	fastDNAml	Construction of phylogenetic trees of DNA sequences using maximum likelihood	online form
	FastMe	A very fast and accurate phylogeny software	FastME Web Page
	Figenix	automates complex pipelines of phylogenetic analysis, gene prediction and EST analysis under the supervision of an expert system	Figenix server
	GAME	Efficient biased estimation of evolutionary distances when substitution rates vary across sites.	website
	Homolens	a database of homologous genes from Ensembl fully sequenced organisms, it allows one to visualize multiple alignments and phylogenetic trees.	Homolens homepage
	Iccare	comparative sequence analysis, mapping information and primer/overgo design	Iccare’s homepage
	IMGT/PhyloGene	Tool for immunoglobulin and T cell receptor variable gene sequences.	IMGT/PhyloGene online
	JaDis	A program for computing distances between nucleic acid sequences.	Jadis homepage
	list of tree softwares	A comprehensive list of tree-softwares for visualisation and manipulations	List
	NARCISSE	Browser of compared genomes	Narcisse online
	neighbor	Neighbor-Joining and UPGMA methods	online form
	NHML	a package inluding programs for maximum-likelihood phylogenetic inferences from DNA sequence data using a non-homogeneous Markov model of DNA sequence evolution.	webpage
	NJplot	A tree drawing program able to draw any phylogenetic tree expressed in the Newick phylogenetic tree format	NJplot homepage
	Phydbac	a web interactive tool that display phylogenomic profiles of bacterial protein sequences	Phydbac online
	PHYLIP	Phylogeny Inference Package	online in Bordeaux
	PhyloJava	A client/server tool dedicated to phylogenetic tree reconstruction.	webpage
	Phylo_win	A graphical colour interface for molecular phylogenetic inference.	Phylo_win’s homepage
	PhyML	A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood	PhyML online
	Principal coordinates analysis	a method for building sequence ordinations using sets of aligned sequences
	protdist	Program to compute distance matrix from protein sequences	online form in Lille
	Q*	A collection of programs aimed at estimating phylogenies from a quartet principle.	webpage
	QR2	a reduction algorithm for approximating a (nonmetric) dissimilarity by a tree distance	QR2 online
	RAP	Phylogenetic Tree Reconciler	webpage
	RRTree	Program for relative-rate tests.	webpage
	SWEEP-BOTT	A program dedicated to the detection of bottlenecks and selective-sweeps from a coalescence-based maximum-likelihood analysis of DNA sequence polymorphism data.	Sweep bott homepage
	TreeGen	Tree generation from distance data.	TreeGen online
	Unrooted	Tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format.	webpage

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Annotation

	Name	Description	Link
	AGMIAL	an integrated system for bacterial genome annotation.	webpage
	EPA	integrated system for EST collection Processing and semi-automatic Annotation	EPA online
	EuGène	an open gene finder for eukaryotic organisms.	webpage
	Exofish	Exon Finding by Sequences Homology	Exofish server
	Figenix	automates complex pipelines of phylogenetic analysis, gene prediction and EST analysis under the supervision of an expert system	Figenix server
	FrameD	A noise-resistant gene finder for prokaryotic and matured eukaryotic sequences	webpage
	GoAnno	Automated annotation of a protein sequence from ontology data extracted from the "Gene Ontology" databank	webpage
	MACSIMS	Multiple Alignment of Complete Sequences Information Management System	online form
	MaGe	Magnifying Genomes - Microbial Genome Annotation System	MaGe homepage
	PRIAM	a method for automated enzyme detection in a fully sequenced genome, based on all sequences available in the ENZYME database.	webpage

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Pattern search

	Name	Description	Link
	Pattern discovery platform	Platform gathering all standard pattern discovery softwares(Pratt, Staden,..) and more original tools (MoDEL, Smile...).	Pattern discovery platform
	Pattern matching platform	Platform gathering pattern matching softwares developped in Symbiose team : STAN and WAPAM and standards tools (PatternN, ScanProsite, ...).	Pattern matching platform
	Pattern search at PRABI	pattern search in a list of sequences selected with WWW-Query
	Pratt	discover patterns conserved in sets of unaligned protein sequences	homepage
	RNAworld	a survey of currently available tools and methods dedicated to DNA/RNA pattern search in genomic sequences	homepage
	Sputnik	DNA microsatellite repeat search utility	online form
	STAN	Suffix-Tree ANalyser (STAN) : looking for nucleotidic and peptidic patterns in chromosomes.	STAN homepage
	WAPAM	Weighted Automata PAttern Matching	Wapam online

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DNA sequences

	Name	Description	Link
	16S rDNA Bacterial Identification	16S bacterial cultures Blast Server	Blast on sequences from cultured bacteria
	AAT - Analysis and annotation tool	Identifies and predicts genes in a DNA sequence by comparing the query sequence against cDNA and protein sequence databases	online form
	BCM Search Launcher	Gene Feature Searches : Exon, Intron, and Gene Model Prediction.	homepage
	BlastSets	New strategy for the representation and the integration of biomolecular knowledge at a cellular scale.	webpage
	CDS search using RecSta	search for coding regions (CDS or exon) in a sequence
	Codon adaptation factor	computes the codon adaptation factor
	Codon frequencies	computes the codons or amino-acid frequencies on a set of sequences previously selected using WWW-Query
	Codon usage index	calculates a codon usage index for a set of genes
	Correspondence analysis	a method suited for studying differenciation among codons or for examining trends in amino-acids composition
	CpG island promoter detection	a mammalian-specific software which proposes to identify the promoter regions associated with CpG islands
	Exofish	Exon Finding by Sequences Homology	Exofish server
	FindTarget	subtractive genome analysis to find bacterial genes of interest	webpage (french)
	GeneID	Program to predict genes, exons, splice sites and other signals along a DNA sequence.	homepage
	GenScan	Predicts the locations and exon-intron structures of genes in genomic sequences from a variety of organisms.	web server at MIT
	Gepeto	GEne Prediction Evaluation TOol	Gepeto online
	IMGT/JunctionAnalysis	Analysis of immunoglobulin and T cell receptor junctions	homepage
	Oligo Heat Map	an online tool to estimate and display hybridizations of oligonucleotides onto DNA sequences	Use Oligo Heat Map
	Oriloc	a program to predict the putative origin and terminus of replication in procaryotic genomes.
	R’HOM	Research of HOMogeneous regions in DNA sequences	homepage
	R’MES	Programs to Find Words with Unexpected Frequencies in DNA Sequences	homepage
	RepeatMasker	returns a masked query sequence ready for database searches as well as a table annotating the masked regions	online form in Bordeaux
	Sarment	sequence segmentation via HMM analysis and Maximal Predictive Partitioning	homepage
	seqinR	an R package devoted to exploratory data analysis and data visualisation of biological sequences	seqinR homepage
	SHOW	Structured HOMogeneities Watcher	homepage
	SNP detection	This system permits the detection via two different strategies : SNP detection in EST databases, and SNP detection in sequences produced by direct DNA sequencing.	webpage
	Tuiuiu	Multiple Repeat Search Filter	Mobyle pipeline

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RNA sequences

	Name	Description	Link
	16S rDNA Bacterial Identification	16S bacterial cultures Blast Server	Blast on sequences from cultured bacteria
	MFOLD	prediction of RNA Secondary Structure by Energy Minimization	Mfold online at Pasteur Paris
	MilPaT	Motifs and Inter-moLecular motifs searching tool using Constraints Solving Problems formAlism and solving Technique	MilPaT online
	RNAworld	a survey of currently available tools and methods dedicated to DNA/RNA pattern search in genomic sequences	homepage
	tRNAscan-SE	detection of transfer RNA genes	Pasteur’s webpage
	Vienna RNA Package	library and several stand-alone programs for the prediction and comparison of RNA secondary structures	online forms at Pasteur Paris

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Proteic analysis

	Name	Description	Link
	Antheprot	Analyse the proteins : package for protein sequence analysis	homepage
	BlastSets	New strategy for the representation and the integration of biomolecular knowledge at a cellular scale.	webpage
	CS-PSeq-Gen	Simulation of protein sequences under constraints	homepage
	CysState	Cysteines disulfide bonding state prediction from protein sequence	CysState online
	FROST	Fold Recognition Oriented Search Tool - usually used when sequence or profile alignment methods such as PSI-BLAST or SAM are unable to find similar sequences	homepage
	GPS@	Bioinformatic Grid web portal dedicated to protein sequence analysis.	GPS@ homepage
	GriPPS	Grid Protein Pattern Scanning	GriPPS homepage
	HCA	Hydrophobic cluster analysis	HCA online
	MPSA	Multiple Protein Sequence Analysis	homepage
	NPS@	Network Protein Sequence Analysis - an interactive Web server dedicated to protein sequence analysis	homepage
	PAT (Protein Analysis Toolkit)	toolkit to facilitate the combination of different processing tools for more complex protein analyses	PAT server
	PredAcc	Prediction of side chains accessibility to solvent	PredAcc online
	Predotar	a neural-network-based prediction program capable of identifying ER signal peptides and mitochondrial or plastid transit peptides	Predotar online
	PSORT	predicts protein subcellular localization sites from their amino acid sequences	online form
	SAPS	Statistical Analysis of Protein Sequences	online form
	seqinR	an R package devoted to exploratory data analysis and data visualisation of biological sequences	seqinR homepage
	SimCT	clustering based on ontologies	webpage
	T-REKS	De novo tandem repeat detection in protein sequences	T-REKS online

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Sequence format conversion

	Name	Description	Link
	abiview	Converts trace files (ABI) into fasta format.	online form
	Mview	visualization of alignments and conversion into different formats (MSF, clustalw, Pearson Fasta, Pir, ...)	online form at Pasteur Paris
	ReadSeq	Multi-format molbio sequence reader	Homepage at IUBio
	Squizz	Sequence/Alignment format checker + converter	Squizz checker
	Sreformat	sreformat program from HMMER package.	online form

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