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LinksTool Listing
| Tool | Version | Description | Documents |
|---|---|---|---|
| Local BLAST | ? | TreeGenes has installed and maintains a local version of the WWW-BLAST server called Local BLAST with databases which are updated weekly. Having a local server offers improved performance and security and allows us to create our own BLAST DBs. | |
| NCBI C Toolkit | ? | The toolkit is used internally at NCBI to process and analyze data from a variety of sources to build and maintain the unified databases and also serves as the components for the end-user applications NCBI distributes. | |
| R | v. 2.6.2 (2008) | R is a language and environment for statistical computing and graphics. | Admin Data_Import_Export Writing_Extensions Introduction Internals Language_Definition |
| bioperl | v. 1.5.2 (2006) | Bioperl is a collection of perl libraries that ease common bioinformatic needs and integrate with common file formats | |
| bl2seq | v. 2.2.17 (2007) | bl2seq is part of NCBI's BLAST package and allows alignment between 2 sequences | ManPage BLAST Readme |
| blastall | v. 2.2.17 (2007) | blastall is part of NCBI's BLAST package and uses all BLAST implementations: blastp, blastn, blastx, tblastx, and tblastn | BLAST Readme ManPage |
| blastclust | v. 2.2.17 (2007) | blastclust clusters both protein and DNA sequences based on resulting BLAST alignments | BLAST Readme Helpfile |
| blastpgp | v. 2.2.17 (2007) | blastpgp is part of NCBI's package and is intended for gapped blastp searches | BLAST Readme Helpfile |
| boxshade | v. 3.2.1 | BOXSHADE provides displya options for multiple alignments from other tools | |
| cap3 | ? (1999) | CAP 3 is a contig assembly program that can take in FASTA formatted sequences and quality scores | Readme |
| clustalw | v. 2.0 (2007) | ClustalW is a multiple alignment utility for DNA and protein sequences | |
| clustalx | v. 2.0 (2007) | windows interface for clustalW | User Manual |
| consed | v. 16.0 (2001) | Consed is a graphical interface for editing phrap output. | Readme |
| emboss | v. 5.0.0 (2007) | EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology user community. EMBOSS integrates a range of currently available packages and tools for sequence analysis into a seamless whole. | About Sequence Formats Command Line Stabdards User Manual |
| ensembl | ? | Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on eukaryotic genomes. | |
| epcr | v. 2.3.7 (2007) | Electronic PCR (e-PCR) is a program for finding STSs in DNA sequences | |
| fbat | v. 1.73 (2006) | FBAT implements a broad class of Family Based Association Tests, adjusted for population admixture. | Manual |
| formatdb | v. 2.2.12 (2005) | Formatdb must be used in order to format protein or nucleotide sourcedatabases before these databases can be searched by blastall, blastpgpor MegaBLAST. | BLAST Readme Readme |
| fpc | v. 8.9.0 (2007) | FPC (fingerprinted contigs) is an interactive program for building contigs from fingerprinted clones, where the fingerprint for a clone is a set of restriction fragments. | Tutorial |
| gap4 | v. 1.6.0 (2005) | Gap4 is a Genome Assembly Program. The program contains all the tools that would be expected from an assembly program plus many unique features and a very easily used interface. It is distributed as part of the Staden package. | |
| genscan | ? | GENSCAN is a general-purpose gene identification program whichanalyzes genomic DNA sequences from a variety of organisms including human, other vertebrates, invertebrates and plants. | |
| gold | v. 1.1.0 (2001) | GOLD (graphical overview of linkage disequilibrium) is a tool for the graphical summary of linkage disequilibrium in genetic data. The summary is well suited to the analysis of dense genetic maps, where contingency tables are cumbersome to interpret. | |
| haplo | v. 3.3.6 (2005) | Haplo uses the EM algorithm to estimate the frequencies of multi-site haplotypes | Manual |
| hmmer | v. 2.3.2 (2003) | find additional homologues of sequence family | Readme UserGuide(PDF) |
| hmmgene | ? | HMMgene is a program for prediction of genes in anonymous DNA. | Usage |
| interproscan | v. 4.3.1 (2007) | protein signature recognition | Readme User Manual |
| joinmap | v. 4.0 (2001) | JoinMap provides high quality tools that allow detailed study of the experimental data and the generation of publication-ready map charts. | Manual (PDF) |
| lagan | v. 2.0 (2003) | The Lagan Tookit is a set of alignment programs for comparative genomics. | |
| mapQTL | v. 5.0 | MapQTL is computer software for the calculation of positions of quantitative trait loci (QTLs) on genetic maps. | Manual (PDF) |
| maskeraid | ? | OBSOLETE : MaskerAid is a drop-in accelerator that increases the speed of RepeatMasker about 30-fold while maintaining sensitivity. | |
| megablast | ? (2005) | nucleotide sequence alignment search | BLAST Readme Helpfile |
| multiclustal | v. 1.1 (2000) | MULTICLUSTAL is a Perl script designed to automate the process of alignment parameter choice for Clustal W with the goal of generating high quality multiple sequence alignments. | Readme |
| njplot | ? (2007) | Phylogenetic tree drawing tool | About |
| phrap | v. 0.990329 | Phrap ("phragment assembly program", or "phil's revised assembly program") is aprogram for assembling shotgun DNA sequence data. | About |
| phred | v. 0.020425.c | 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. | Documentation |
| phylip | v. 3.66 | A package of tools: PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). | User Manual Primer (PDF) |
| phyml | ? (2003) | Phyml is a program that constructs phylogenetic trees from sequence alignments using the maximum likelihood method. | Web Manual Command Line Manual |
| plato | v. 2.11 | detect recombination and selection | Manual |
| polybayes | v. 3.0 (2001) | PolyBayes is a computer program for the automated analysis of single-nucleotide polymorphism (SNP) discovery in redundant DNA sequences. | |
| polyphred | v. 5.04 (2006) | PolyPhred identifies substitution SNPs as potential heterozygotes by comparing traces in a sequence assembly. | Manual |
| probconsRNA | v. 1.12 | ||
| puzzleboot | v. 1.03 | Puzzleboot is a UNIX shell script facilitating bootstrap analysis using TREE-PUZZLE and PHYLIP. It enhances TREE-PUZZLE by allowing one to analyse multiple datasets, and an be used for both protein and DNA distance bootstrap analysis. | Readme |
| qtdt | v. 2.6.0 (2007) | Test linkage disequilibrium | |
| readseq | v. 2.1.22 (2005) | Reads and writes nucleic/protein sequences in various formats. Data files may have multiple sequences. | |
| repeatmasker | v. 3.1.9 (2008) | Screens DNA sequences for interspersed repeats and low complexity DNA sequences. | Manual |
| rnabob | v. 2.1 | The program "rnabob" searches for RNA motifs in sequence databases.Rather than searching simply for primary sequence matches, rnaboballows one to search for secondary and tertiary structural motifs aswell. | |
| rnamot | v. 2.1 | The RNAMOT program finds primary or secondary structure motifs in nucleic acid sequences. | |
| rpsblast | ? (2005) | RPS-BLAST (Reverse PSI-BLAST) searches a query sequence against a database of profiles, or score matrices, prepared by copymat, producing BLAST-like output. | BLAST Readme Helpfile |
| seaview | v. 2.2 (2005) | A graphical multiple sequence alignment editor. | |
| sequin | v. 7.90 | Sequin is a program designed to aid in the submission of sequences to the GenBank, EMBL, and DDBJ sequence databases. | Help QuickGuide |
| sim4 | ? | Sim4 is a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene. | Helpfile |
| sputnik | ? (2003) | Sputnik searches DNA sequence files in Fasta format for microsatellite repeats. | |
| staden | v. 1.6 | The Staden Package is a suite of tools for: sequence assembly, analysis, and mutation detection. | |
| structure | v. 2.2 (2007) | Structure implements a model-based clustering method for inferring population structure using genotype data consisting of unlinked markers. The methods used are introduced in a paper by Pritchard, Stephens and Donnelly (2000) | Manual (PDF) |
| tree-puzzle | v. 5.2 (2004) | Tree-puzzle is a program that constructs phylogenetic trees from sequence alignments using the maximum likelihood method. | Manual (PDF) |
| twinscan | v. 4.1.2 (2007) | predicting gene structure | |
| vista | ? | VISTA is an application that allows the visualization of long sequence alignments with annotation information. | |
| weighbor | v. 1.2 | Weighbor is a tool for building phylogenetic trees from distance matrices. It employs a weighted version of the neighbour-joining method in which longer distances in the matrix are given less weight. | Helpfile |
| wise2 | v. 2.2.0 (2002) | Wise2 is a package focused on comparisons of DNA sequence and protein sequence. | Manual |
| wublast | v. 2.0 (2006) | Washington University BLAST - performs sensitive, selective and rapid similarity searches of protein and nucleotide sequence databases. | Manual |
| xgrail | ? | GRAIL is a suite of tools designed to provide analysis and putative annotationof DNA sequences both interactively and through the use of automated computation. | |
| zt | ? (2001) | ZT is a tool which performs simple and partial Mantel tests. The partial Mantel test investigates the correlation between two matrices while controlling the effect of a third one, and thus tries to remove spurious correlations. |
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