| description | AMOS is collection of tools and class interfaces for the assembly of DNA sequencing reads. |
| version | 2.0.8 |
| description | Artemis is a genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation. |
| version | 11 |
| description | Bayesian Analysis in Molecular Biology and Evolution. |
| version | 4.01 |
| description | BIONJ is a distance based phylogeny reconstruction algorithm, which is well suited for distances estimated from DNA or protein sequences. |
| version |
| description | The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. |
| version | 2.2.21 |
| description | Taxonomy report from a blast report |
| version | 1.2 |
| description | Extract identifier of blast hits (from the summary) and make a list in USA format |
| version | 1.0 |
| description | Washington University BLAST (WU BLAST) is a powerful software package for gene and protein identification, using sensitive, selective and rapid similarity searches of protein and nucleotide sequence databases. |
| version | 2.0 (20060504) |
| description | Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. |
| version | 1.0 |
| description | Bowtie is an ultrafast, memory-efficient short read aligner. |
| version | 0.9.8 |
| description | BOXSHADE is a program for pretty-printing multiple alignment output. |
| version | 3.3.1 |
| description | DNA sequence assembly program. |
| version |
| description | Small tools for sequencer trace data. |
| version | 0.99 |
| description | Cut dna region in frame |
| version | 0.2.1 |
| description | ClonalFrame is a computer package for the inference of bacterial microevolution using multilocus sequence data |
| version | 1.1 |
| description | ClustalW is a general purpose multiple alignment program for DNA or proteins. |
| version | 2.0.12 |
| description | ClustalX is a new windows interface for the ClustalW multiple sequence alignment program. |
| version | 2.0.12 |
| description | CodonW is a program designed to simplify the Multivariate analysis (correspondence analysis) of codon and amino acid usage. |
| version | 1.4.4 |
| description | ComAlign is a program, that given a number of sequences, generates a number of heuristic alignments and combines these best possible. |
| version |
| description | The program combat implements the method for combined DNA/protein alignment. |
| version | 1.0 |
| description | Concatanation of two fasta files with same identifier |
| version | 1.00 |
| description | Consed is a tool for viewing, editing, sequence assemblies created with phrap. |
| version | 19 |
| description | CONSEL calculates the p-value using several testing procedures; the bootstrap probability, the Kishino-Hasegawa test, the Shimodaira-Hasegawa test, and the weighted Shimodaira-Hasegawa test. In addition to these conventional tests, CONSEL calculates the p-value based on the approximately unbiased test using the multi-scale bootstrap technique. |
| version | v0.1k |
| description | The CONSENSUS programs are a collection of programs for determining and analyzing DNA and protein patterns describing functional elements. |
| version |
| description | Clustal Ouput Structural Analysis. |
| version |
| description | Small collection of programs to manipulate databanks files. |
| version | 0.99a |
| description | Divide-and-Conquer Multiple Sequence Alignment (DCA) is a program for producing fast, high quality simultaneous multiple sequence alignments of amino acid, RNA, or DNA sequences. |
| version | 1.1 |
| description | DIALIGN is a software program for multiple alignment. |
| version | 2.2.1 |
| description | A dot-matrix program with interactive greyscale rendering for genomic DNA and Protein sequence analysis. |
| version | 3.1 |
| description | Definition of secondary structure of proteins given a set of 3D coordinates. |
| version | 2000 |
| description | EagleView is an information-rich genome assembler viewer with data integration capability. |
| version | 1.83 |
| description | Compute synonymous sequences that maximize protein evolutionary landscape exploration. |
| version | 1.0 |
| description | EMBOSS is "The European Molecular Biology Open Software Suite", a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. |
| version | 6.2.0 |
| description | Extracts translation(s) from a Genbank or Embl entry. |
| version |
| description | The FASTA package provides a modular set of sequence comparison programs. |
| version | 3.6 (x4) |
| description | fastDNAml is a program for estimating maximum likelihood phylogenetic trees from nucleotide sequences. |
| version | 1.2.2 |
| description | Genetic Analysis Software |
| version | 4.1P |
| description | ClustalW is a general purpose multiple alignment program for DNA or proteins. |
| version | 1.2.2 |
| description | Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. |
| version | 0.91b |
| description | GCG is an integrated package of over 150 programs that allows you to manipulate and analyze nucleic acid and protein sequences. |
| version | 11.0 |
| description | The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. |
| version | 1.3.0 |
| description | Identification of complete gene structures in genomic DNA. |
| version | 1.0 |
| description | GigaBayes is a short-read SNP and short-INDEL discovery program. |
| version | beta |
| description | Golden is a small databanks entries retriever. |
| version | 1.1a |
| description | Sequence-based Prediction of Minimum Generation Times for Bacteria and Archaea |
| version | v1.05 |
| description | Clusters of binding sites. |
| version | 1.0 |
| description | HMMER is an implementation of profile HMM methods for sensitive database searches using multiple sequence alignments as queries. |
| version | 3.0b2 |
| description | Prediction of transmembrane helices and topology of proteins. |
| version | 2.1 |
| description | html4blast is a simple Text to HTML blast results formatter |
| version | 1.6a |
| description | Package for using multi-locus genotype data to investigate population structure. |
| version | 20070713 |
| description | Inference of RNA secondary structure alignments "covariance models" (CMs) |
| version | 1.00 |
| description | Ktreedist calculate the minimum branch length distance (or K tree score) from one phylogenetic tree to another. The K tree score provides a measure of the difference in both topology and branch lengths between two trees after scaling one of them to have a global divergence as similar as possible to the other tree. |
| version | 1 |
| description | software for finkage and Association Modeling in Pedigrees. LAMP uses a maximum likelihood model to extract information on genetic linkage and association from samples of unrelated individuals, sib pairs, trios and larger pedigrees |
| version | 0.0.9 |
| description | Manipulation Environment for Genetic Analyses. |
| version | 2.4.5 |
| description | LVB uses parsimony to reconstruct phylogeny from a nucleotide alignment, using a simulated annealing heuristic search. |
| version | 2.2 |
| description | Programs for genetic linkage analysis and mapping genes underlying complex traits. |
| version | 3 |
| description | Maq is a software that builds mapping assemblies from short reads generated by the next-generation sequencing machines. |
| version | 0.7.1 |
| description | Maqview is graphical read alignment viewer |
| version | 0.2.5 |
| description | Mauve is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion |
| version | 2.3.1 |
| description | Cluster algorithm for graphs |
| version | 09-182 |
| description | Manipulation Environment for Genetic Analyses. |
| version | 4.5.1 |
| description | Melting computes, for a nucleic acid duplex, the enthalpy, the entropy and the melting temperature of the helix-coil transitions. |
| version | 4.2g |
| description | MERLIN uses sparse trees to represent gene flow in pedigrees. |
| version | 1.1.2 |
| description | RNA and DNA secondary structure prediction using nearest neighbor thermodynamic rules. |
| version | 3.2 |
| description | Computer Program Package for Molecular Phylogenetics. |
| version | 2.3b2 |
| description | MOSAIK is a suite comprising of three modular programs: MosaikBuild, MosaikAligner, and MosaikAssembler. |
| version | beta2007 |
| description | Modular sofwate system for microbial ecology studies |
| version | 1.7.2 |
| description | MrBayes is a program for the Bayesian estimation of phylogeny. |
| version | 3.1.2 |
| description | mreps is a software for identifying serial repeats (usually called tandem repeats) in DNA sequences. |
| version | 2.5 |
| description | MSA is a program to do multiple sequence alignment under the sum-of-pairs criterion. |
| version | 2.1 |
| description | MSPcrunch, a filtering tool for Blast matches. |
| version | 2.5 |
| description | This software will allow you to align simultaneously several biological sequences. |
| version | 5.4.1 |
| description | MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form |
| version | 3.22 |
| description | Multiple alignment software for protein and nucleotide sequences. |
| version | 3.7 |
| description | MView reformats the results of a sequence database search (BLAST, FASTA, etc) or a multiple alignment (MSF, PIR, CLUSTAL, etc) adding optional HTML markup to control colouring and web page layout. |
| version | 1.49 |
| description | NJplot is a tree drawing program able to draw any phylogenetic tree expressed in the Newick phylogenetic tree format. |
| version | 20051109 |
| description | Solexa Off-Line Basecaller Software |
| version | 1.6 |
| description | Genome-scale oligonucleotide design for microarrays. |
| version | 2.1.4 |
| description | A Python Package for Phylogenetics |
| version | 0.87.r132 |
| description | Software package for inference of evolutionary trees. |
| version | 4b10 |
| description | Tools for the statistical analysis of family-based association studies. |
| version | 3.5 |
| description | PEDSTATS is a tool for quick validation and summary of any pair of pedigree and data files. |
| version | 0.6.10 |
| description | CNV detection from Illumina whole-genome SNP genotyping arrays. It has been extended to handle candidate gene SNP arrays, to handle recent high-density arrays with non-polymorphic markers (so-called CN markers), and to handle Affymetrix genome-wide arrays. |
| version | 2009.08.27 |
| description | Encapsulate penncnv package scripts (kcolumn, detect_cnv, visualise_cnv) and parallelize multiple jobs with sge |
| version | 1.0 |
| description | The pftools package contains programs for generalized profile applications. |
| version | 2.3 |
| description | Software for haplotype reconstruction, and recombination rate estimation from population data. |
| version | 2.1.1 |
| description | phrap is a program for assembling shotgun DNA sequence data. |
| version | 1.080721 |
| description | The phred software reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base. |
| version | 071220.b |
| description | PHYLIP is a package of programs for inferring phylogenies. |
| version | 3.67 |
| description | PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments. |
| version | 2.3c |
| description | PHYML - A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. |
| version | 3.0 |
| description | Pattern-Induced Multi-sequence Alignment program. Performs a multi-sequence alignment of a set of (presumably related) sequences using an extension of our covering pattern construction algorithm. |
| version | 1.40 |
| description | analysis of genotype/phenotype data |
| version | 1.07 |
| description | PolyPhred is a program that compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions. |
| version | 5.04 |
| description | Pattern discovery tool. |
| version | 2.1 |
| description | Protein secondary structure prediction software. |
| version | 2.1.2 |
| description | A Computer Program for Automatically Selecting PCR Primers |
| version | 0.5 |
| description | PCR primer design tool. |
| version | 1.0.0 |
| description | Primer design software (mostly derived from primer 0.5). |
| version |
| description | Search for Prosite patterns in protein sequences. |
| version | 0.02a |
| description | PSORT is a program for the prediction of protein localization sites in cells. |
| version | 981201 |
| description | Program for bacterial protein subcellular localization prediction. |
| version | 2.1.0 |
| description | TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. |
| version | 5.2 |
| description | Linkage Disequilibrium Analyses for Quantitative and Discrete Traits. |
| version | 2.5.1 |
| description | Software program for generating space-filling pictures of molecules from PDB files. |
| version | 2.1 |
| description | QuantiSNP identifies putative copy number alterations from Illumina Infinium I/II SNP genotyping data. |
| version | v2.3 beta |
| description | QuickTree is a program for the rapid reconstruction of phylogenies by the Neighbor-Joining method. |
| version | 1.1 |
| description | Report bootstrap values found with consensus program (after bootstrap analysis) on related tree found with phylogeny algorithm without bootstrap analysis. |
| version | 1.00 |
| description | RELPAIR is a program that infers the relationships of pairs of individuals based on genetic marker data, either within families or across an entire sample. |
| version | 2.0.1 |
| description | RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. |
| version | 3.1.5 |
| description | Perform ab initio method to detect multiple repeats in genomes |
| version | 1 |
| description | A method for fast database search for all k-nucleotide repeats |
| version |
| description | SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. |
| version | 0.1.7a |
| description | Methods and algorithms for statistical analysis of protein sequences. |
| version |
| description | Genomewide identification of cisregulatory motifs and modules underlying gene coregulation using statistics and phylogeny |
| version | 1.0 |
| description | Search for patterns in DNA and protein sequences. |
| version | 97 |
| description | SeaView is a graphical multiple sequence alignment editor. |
| version |
| description | SEG programs filter low complexity regions in sequences. |
| version |
| description | Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process. |
| version | 1.3.2 |
| description | Split up query into smaller overlapping chunks |
| version |
| description | Short read mapping against a target genome |
| version | 1.46 |
| description | Multiple Prosite motifs searching. |
| version | 1.0 |
| description | A coalescent program for the simulation of complex recombination patterns over large genomic regions under various demographic models. |
| version | 2.1.2 |
| description | SimWalk2 is a statistical genetics computer application for haplotype, parametric linkage, non-parametric linkage (NPL), identity by descent (IBD) and mistyping analyses on any size of pedigree. |
| version | 2.91 |
| description | SMILE is a tool that infers motifs in a set of sequences, according to some criterias. |
| version | 1.47 |
| description | Program for estimating frequencies of haplotypes of large numbers of diallelic markers from unphased genotype data from unrelated subjects. |
| version | 1.3.1 |
| description | Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. |
| version | 1.1 |
| description | SOLAR is a package for genetic variance components analysis, including linkage analysis, quantitative genetic analysis, and covariate screening. |
| version | 4.1.5 |
| description | Sequence/Alignment format checker. |
| version | 0.99 |
| description | Data analysis and statistical software. |
| version | 10.0.1 |
| description | Package for using multi-locus genotype data to investigate population structure. |
| version | 2.2.2 |
| description | tacg is a command-line program that performs many of the common routines in pattern matching in biological strings. |
| version | 4.1.0 |
| description | A program to estimate the rate of molecular evolution and time-scale of a phylogeny from dated sequences. |
| version | 1.2 |
| description | Transmembrane topology prediction. |
| version | 1.00 |
| description | Aligns and finds the phylogeny at the same time for a set of homologous proteins or DNA/RNA sequences. |
| version |
| description | tRNA detection in large-scale genome sequence. |
| version | 1.23 |
| description | T-Coffee is a multiple sequence alignment package. |
| version | 3.93 |
| description | VAAL is a polymorphism discovery algorithm for short reads |
| version | 1.6 |
| description | Sequence assembler for very short reads |
| version | 1.0.03 |
| description | RNA Secondary Structure Prediction and Comparison. |
| version | 1.7 |
| description | Weighted Neighbor Joining. |
| version | 1.2.1 |
| description | Versatile molecular modelling package that is specialized on working with proteins and the molecules in their environment like water, ligands, nucleic acids, etc. |
| version | 20080408 |
| description | Wise2 is a package focused on comparisons of bio polymers, commonly DNA sequence and protein sequence. |
| version | 2.0 |
| description | Software for exon trapping. |
| version |
| description | This software is able to extract putative cassette structures that fulfill the criteria established from analysis of previously known cassettes from integrons and superintegrons. |
| version | 3.03 |