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专业背景:计算机科学 研究方向与兴趣: JavaEE-Web软件开发, 生物信息学, 数据挖掘与机器学习, 智能信息系统 目前工作: 基因组, 转录组, NGS高通量数据分析, 生物数据挖掘, 植物系统发育和比较进化基因组学

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生物信息学在线分析工具之Alignments - Phylogeny  

2010-01-05 19:35:36|  分类: 生信分析软件 |  标签: |举报 |字号 订阅

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  • Alignments
    • ALIGN (alignment of 2 sequences : fasta)IGHM(France)
    • Align Two Polypeptide Chains by Combinatorial ExtensionSDSC(USA)
    • Align two sequencesSBDS(UK)
    • Align two sequencesUSC(USA)
    • Alignment ComparisonUCSC(USA), see alsotuneup, see alsodna-rna
    • Alignment Tools (Pasting, Inter-block, Consensus, Clustalw)EMBL-Bork(Germany)
    • ALion (Pairwise protein sequence alignment using Needleman-Wunsch or Smith-Waterman algorithms)Stanford(USA)
    • AllAllETH(Switzerland)
    • AltAVisT (Alternative Alignment Visualization Tool)Bielefeld(Germany)
    • AMAS (read an alignment to enhance conserved aminoacids)Barton group(UK)
    • AVID (align two sequences)Berkeley(USA), anotherlink
    • Blast 2 sequences (alignment using blast)NCBI, see alsoUMMS, see alsoPasteur, see alsoToulouse
    • BLock Gap Sizes (calculates inter-block gap sizes for blocks in a CLUSTAL multiple alignment)EMBL(Germany)
    • Clustalw
    • Clustalw 1.6
    • Clustalw 1.7
    • Clustalw 1.8
    • ComAlign: Combining many multiple alignments in one improved alignmentPasteur(France)
    • Consensus (calculates the consensus for the CLUSTAL or MSF multiple alignment)EMBL(Germany)
    • Consensus (alignment for reliable framework prediction in homology modeling)Boston(USA)
    • CRASP (Correlation Analysis of Sequences of Proteins)MBS(Russian)
    • DBA (Dna Block Aligner)Sanger(UK)
    • DbClustal (Align your Protein to the Blast Top Sequences found in SPtrEMBL)Strasbourg(French)
    • DCA (Divide-and-Conquer Multiple Sequence AlignmentBielefeld(Germany)
    • DIALIGNBielefeld(Germany), see alsoGSF(Germany), see alsoPasteur(France)
    • DRUID (localization of recombination breakpoints in an alignment of sequences)Pasteur(French)
    • DSC (Multiple alignment and structure prediction)ICRF(UK)
    • EST2GENOME (align EST and genomic DNA sequences)Pasteur(France)
    • ESTScanEMBNet, seeV2
    • Filtersites (Filter conserved sites in an alignment)Pasteur(French)
    • GraphAlignNMSU(USA)
    • HYPERMUT (detecting hypermutations in viral sequences with an emphasis on G -> A hypermutation)LANL(USA)
    • ITERALIGNv1.1 (multiple alignment of protein sequences)Stanford(USA)
    • K2 (protein structure alignment program)ZLab(USA)
    • LAGAN Alignment Toolkit (Lagan, M-Lagan, Chaos)Stanford(USA)
    • LALIGN (alignment of 2 sequences)CRBM(France), see alsoEMBNet, see alsoVirginia
    • LAMA (Local Alignment of Multiple Alignments: Block vs Block Searcher)FHCRC(USA)
    • LASSAP (LArge Scale Sequence compArison Package)Pasteur(France)
    • LFasta (Local Alignment Tool for Nucleic Sequences)ACNUC(France)
    • LGA (method for finding 3D similarities in protein structures)LLNL(USA)
    • MASIA (recognition of common patterns and properties in multiple aligned protein sequences)Texas(USA)
    • Match-Box serverFUNDP(Belgium), results bye-mail
    • MATCHER (inds the best local alignments between two sequences)Pasteur(France)
    • MatrixPlot (generate mutual information plots of sequence alignments)CBS(Denmark)
    • MAVID (multiple alignment)Berkeley(USA)
    • MBS AlignerMBS(USA)
    • MGAlignIt (align mRNA sequences to genomic sequences)Singapore
    • MSA (Ctree, MSA, Clustal)Michigan(USA)
    • MULALBLA (Multiple alignment with Blast)U-ParisSud(French)
    • MultAlign (Options : Score, GapAdjust, ProbModel, RootedTree, MSA ..)ETHZ(Switzerland)
    • MultalinPBIL(France)
    • MultalinLGC(French)
    • MultalinToulouse(French)
    • Multiple alignement (GeneBee)Moscou
    • Multiple Sequence Alignment (MAP)Michigan(USA)
    • Multiple Sequence AlignmentNYU(USA)
    • Multiple Sequence Alignments (Clustalw1.7, Map, Pima, Block Maker, Meme, MatchBox)BCMLauncher
    • NEEDLE (Needleman-Wunsch global alignment)Pasteur(France)
    • Pairwise Global AlignmentNYU(USA)
    • Pairwise Sequence Alignment (SIM, GAP, NAP)Michigan(USA)
    • Pairwise Sequence Alignment (SIM, ALIGN, BLAST, LAP2, PCWISE, PCWISE)BCM
    • Pairwise Sequence Alignment (Bayesian Algorithm)RPI(USA)
    • PIMA (Align a Query Sequence against a PIMA Multiple Alignment using PIMA)BCM
    • PIMA (Pattern-Induced Multi-sequence Alignment program)Pasteur(French)
    • PipMaker and Multi-PipMaker (alignments of similar regions in two DNA sequences, or more)Pennsylvania(USA)
    • PLALIGN (alignment of 2 sequences)Virginia
    • POA (Multiple Sequence Alignment Using Partial Order Graphs)UCLA(USA)
    • Praline (Multiple Sequence Alignment with many options)NIMR(USA)
    • PRSS (evaluate the significance of a protein or DNA sequence similarity score)EMBNet
    • RevTrans (constructing alignments of coding DNA from aligned amino acid sequences)CBS(Denmark)
    • SAMUCSC( linear hidden Markov model),documentation, see alsoPasteur
    • SEA (protein pairwise alignment based on network matching algorithm)California(USA)
    • SIM : Alignment Tool for 2 sequencesprotein sequences,nucleic sequences(Expasy)
    • SIM4 (to align cDNA and genomic DNA)PBIL(French)
    • Spidey (mRNA-to-genomic alignment program)NCBI(USA)
    • SSEARCH Pairwise Sequence AlignmentPIR(USA)
    • SSAS (Secondary Structure Alignment Server)Rutgers(USA)
    • SSPA - Significant Segment Pair AlignmentStanford(USA)
    • STRETCHER (finds the best global alignment between two sequences)Pasteur(France)
    • SUPERMATCHER (finds a match of a large sequence against one or more sequences)Pasteur(France)
    • T-COFFEE (Multiple Alignments)EMBNET, see asloCMBI, see alsoIGS
    • ToPLign (standard pairwise and multiple alignment methods)GMD(Germany)
    • WATER (Smith-Waterman local alignment)Pasteur(France)
    • WORDMATCH (finds all exact matches of a given size between 2 DNA sequences)Pasteur(France)
    • ZPREDLICR(MultPredict Secondary Structure of Multiply Aligned Protein Sequences : format de l'alignement AMPS)
  • Phylogeny - Evolution
    • AllAll (see alsoTreeGen)ETHZurich
    • BAMBE (Bayesian Analysis in Molecular Biology and Evolution)Pasteur(France), see alsoDuquesne(USA)
    • Bayesian Phylogenetic FootprintWadsworth(USA)
    • BIONJ (an improved version of the NJ algorithm)Pasteur(France)
    • FastDNAmlPasteur, see alsoadvanced form, see alsoInfoBioGen
    • Gblocks (eliminates poorly aligned positions and divergent regions of a DNA or protein alignment for phylogenetic analysis)EMBL(Germany)
    • LVB (Reconstructing Evolution With Parsimony And Simulated Annealing)Pasteur(French)
    • Molphy (ProtML, NucML, ProtST, NJDist)Pasteur(France)
    • PhyloBLAST (facilitating phylogenetic analysis of BLAST results)Vancouver(Canada)
    • Phyloblock (align sequences and build a tree)ANL(USA)
    • Phylodendron (phylogenetic tree printer)IUBIO(USA)
    • Phyloquart (parciquart, distquart, qstar, addquart)Pasteur(France)
    • Phylogenetic tree prediction (from an alignment)Moscow
    • Phylogenetic Web ProfilerGSF(Germany)
    • PHYLIP
    • Principal Coordinates AnalysisLyon(French)
    • Puzzle (Tree reconstruction for sequences by quartet puzzling and maximum likelihood)Pasteur, advancedform(French), see alsokun
    • Pyramids (pyramidal analysis tool for sequence clustering)Pasteur(French)
    • QR2Pasteur(French)
    • Quicktree (Rapid reconstruction of phylogenies by the Neighbor-Joining method)Pasteur(French)
    • RecPars (Parsimony analysis of DNA sequences)Aarhus(Denmark)
    • RETREE (unroot a tree)Pasteur(French)
    • RIO (resampled inference of orthologs)St Louis(USA)
    • ROSE (Random-model Of Sequence Evolution)Bielefeld(Germany)
    • SeqGen (Simulation of DNA sequence evolution)Pasteur(France)
    • SHOT (Shared Ortholog and Gene Order Tree Reconstruction Tool)Heidelberg(Germany)
    • SNAP (calculates synonymous and non-synonymous substitution rates based on a set of codon-aligned nucleotide sequences)LANL(USA)
    • SplitsTree 2Bielefeld(Germany)
    • The Transformation Distance (A dissimilarity measure based on large mutations)Lille(France)
    • Weighbor (Weighted neighbor joining)Pasteur(France)
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