Multiple Sequence Alignment Clustal Omega from EMBI-EBI Job Dispatcher Source codes (The original Clustal website, clustal.org, has been retired and no longer available) How Des Higgins developed Clustal programs: "The story of Clustal: democratising sequence alignments" ClustalW @ GenomeNet ClustalW @ prabi ClustalX (GUI version of ClustalW with more functions) with Qt 5 MUSCLE (v5 and also legacy v3) by Robert Edgar MUSCLE 5 from EMBI-EBI Job Dispatcher MUSCLE (legacy version) from EMBI-EBI Job Dispatcher MAFFT by Kazutaka Katoh from EMBI-EBI Job Dispatcher T-Coffee (including M-Coffee, Expresso, etc.) from EMBI-EBI Job Dispatcher Kalign2 from EMBI-EBI Job Dispatcher PRALINE PROMALS PROMALS3D ProbCons: Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences ProbCons @ Phylogeny.fr CONTRAlign: CONditional TRAining for Protein Sequence Alignment Probalign: Multiple sequence alignment using partition function posterior probabilities MSAProbs: Parallel and accurate multiple sequence alignment QuickProbs 2: faster successor of MSAProbs PnpProbs: Progressive and non-progressive combined alignment method FSA: Fast Statistical Alignment (sourceforge version) COBALT: Constraint-based Multiple Alignment Tool at NCBI hmmalign (part of HMMER package, requires a profile HMM to be aligned against) DIALIGN (Anchored DIALIGN, CHAOS-DIALIGN, and DIALING-TX) by Burkhard Morgenstern DCA: Divide-and-Conquer Multiple Sequence Alignment by J. Stoye OPAL MultAlin by Florence Corpet PRANK: Phylogeny-aware progressive sequence alignment method webPRANK from Goldman group @ EMBI-EBI PAGAN: Multiple sequence alignment using partial-order graphs (based on the principle same as PRANK) ProGraphMSA (similar to PAGAN, incorporates a graph-based sequence representation combined with the phylogeny-aware gap placement algorithm of PRANK) learnMSA: Learning and Aligning large Protein Families Simultaneous Alignment and Phylogeny SATé - Simultaneous Alignment and Tree Estimation PASTA - Practical Alignment using Saté and TrAnsitivity MAGUS: Multiple sequence Alignment using Graph clUStering UPP2 - Ultra-large alignments using Phylogeny-aware Profiles BAli-Phy: Baysian ALignment and Phylogeny estimation Canopy: Parallelised iterative search of optimal phylogeny and phylogeny-aware sequence alignment Alignment Visualization and Editors SuiteMSA: Visual Tool for Multiple Sequence Alignment Comparison and Molecular Sequence Simulation ClustalX (GUI version of ClustalW with more functions) with Qt 5 AliView (fast alignment editor/viewer) SeaView (including phylogenetic reconstruction/viewer) Jalview: a multiple alignment editor written in Java Wasabi: a powerful multiple sequence alignment browser (includes ancestral sequence reconstruction) MEGA: Molecular Evolutionary Genetics Analysis (includes an alignment editor) STRAP: Interactive Structure based Sequences Alignment Program Kalignvu: an lighweight viewer for multiple sequence alignments and phylogenetic trees Squint Se-Al (only for Mac OS X up to 10.6) BioEdit: Biological sequence alignment editor for Win95/98/NT/2K/XP/7 GeneDoc: a multiple alignment editor for Windows Translated DNA Alignment TranslatorX RevTrans 2.0 PAL2NAL tranalign (from EMBOSS server) tranalign (from another EMBOSS) Alignment Trimmming/Filtering Gblocks from NGPhylogeny.fr BMGE from NGPhylogeny.fr Noisy from NGPhylogeny.fr trimAl trimAl from NGPhylogeny ClipKIT HmmCleaner PREQUAL Divvier Alignment Evaluation BAliBASE 4: Benchmark Alignment dataBASE (including bali_score) HOMSTRAD: Homologous Structure Alignment Database BENCH from MUSCLE (including BAliBASE, PREFAB, OXBENCH, and SABRE) Guidance2 Veralign Mumsa AlignStat QuanTest Phylogeny Reconstruction IQ-TREE PhyML RAxML: Randomized Axelerated Maximum Likelihood (and other software from Exelixis Lab) RAxML-NG: Randomized Axelerated Maximum Likelihood (and other software from Exelixis Lab) FastTree 2: Approximately-maximum likelihood trees for large alignments MrBayes: Bayesian Inference of Phylogeny Phylip GARLI: Genetic Algorithm for Rapid Likelihood Inference FastME: Fast and accurate phylogeny reconstruction algorithm based on the minimum-evolution principle BioNJ: an improved version of the NJ algorithm based on a simple model of sequence data SplitsTree: Software for computing phylogenetic networks T-Rex: Tree and Reticulogram reconstruction Phylogeny Visualization FigTree: a graphical viewer of phylogenetic trees ITOL: Interactive Tree of Life IcyTree Evolview3 TreeDyn: Towards dynamic graphics and annotations for analyses of trees Newick Display @ NGPhylogeny.fr NJplot Phylo.io: A web app and library for visualising and comparing phylogenetic trees Phylo.io (a newer version) ARB: a software environment for sequence data (including alignment/phylogeny viewers and more) Treevolution Archaeopteryx: Visualization, Analysis, and Editing of Phylogenetic Tress (the successor to ATV) A list of phylogenetic tree visualization software Alignment to Phylogenetic Analysis Pipeline CIPRES: Cyberinfrastructure for Phylogenetic Research (including mafft, BAli-Phy, RAxML, MrBayes, GARLI, PAUP, etc.) NGPhylogeny.fr (including mafft, MUSCLE, Clustal Omega, BMGE, Gblocks, trimAL, PhyML, MrBayes, FastME, TNT, etc.) Phylogeny.fr (including MUSCLE, ProbCons, T-Coffee, ClustalW, Gblocks, PhyML, NJ, BioNJ, MrBayes, TNT) Phylomon2 (including MUSCLE, ClustalW, Lagan, MLagan, trimAl, PhyML, MrBayes, etc.)