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Phylogeny Reconstruction Bioinformatics Tools and Software Online.
| CIPRes - http://www.phylo.org/ The Cyberinfrastructure for Phylogenetic Research (CIPRes) project aims to develop a computational infrastructure for systematics. Other goals of the project include providing a central resource enabling computational systematics and education and traini - [Read more CIPRes] |
| Codon Usage Database - http://www.kazusa.or.jp/codon/ Find GC content and frequency of codon usage for any organism that has a sequence in GenBank. - [Read more Codon Usage Database] |
| Joes Site - Phylogeny Programs - http://evolution.genetics.washington.edu/phylip/software.html Comprehensive list of phylogeny packages, compiled by Joe Felsenstein, creator of Phylip. - [Read more Joes Site - Phylogeny Programs] |
| MEGA - http://www.megasoftware.net/ MEGA (Molecular Evolutionary Genetics Analysis) is a software package for phylogenetic analysis with a graphical user interface. It allows viewing and editing of the aligned input sequence data and provides many tools for phylogenetic and statistical ana - [Read more MEGA] |
| Mesquite - http://mesquiteproject.org/mesquite/mesquite.html Mesquite is an open source software project designed to deal with comparative data about organisms and evolutionary analyses. Mesquite contains modules for phylogenetic analysis, population genetics, and non-phylogenetic multivariate analysis. - [Read more Mesquite] |
| NCBI Taxonomy Database - http://www.ncbi.nlm.nih.gov/Taxonomy Taxonomic classification of all organisms with sequences in GenBank. - [Read more NCBI Taxonomy Database] |
| NJplot - http://pbil.univ-lyon1.fr/software/njplot.html NJplot is a tool for visualizing binary trees such as the phylogenetic trees output from the PHYLIP programs. Availiable for several platforms including Windows, MacOS, Linux and Solaris. - [Read more NJplot] |
| Orthologue Search Service - http://dove.embl-heidelberg.de/Blast2e/ BLAST a protein sequence then perform automated phylogenetic analysis to detect orthologous sequences. - [Read more Orthologue Search Service] |
| PHYLIP - http://evolution.genetics.washington.edu/phylip.html Comprehensive set of programs for phylogenetic analyses; available for PC and Mac; source code available for easy compiling in UNIX. - [Read more PHYLIP] |
| PhyloBLAST - http://www.pathogenomics.bc.ca/phyloBLAST/ BLAST a protein sequence, then perform automated phylogenetic analysis on hits or on uploaded sequences; PHYLIP-based analyses. - [Read more PhyloBLAST] |
| PHYML - http://atgc.lirmm.fr/phyml/ Phyml is a program that constructs phylogenetic trees from sequence alignments using the maximum likelihood method. - [Read more PHYML] |
| Puzzleboot - http://hades.biochem.dal.ca/Rogerlab/Software/software.html#puzzleboot 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 can be used for both protein and DNA distance bootstrap analysis. - [Read more Puzzleboot] |
| Ribosomal Database Project - http://rdp.cme.msu.edu/ Highly curated database of aligned and annotated rRNA sequences with accompanying phylogenies; data available for download. - [Read more Ribosomal Database Project] |
| Tree of Life - http://phylogeny.arizona.edu/ Multi-authored project attempting to represent online the entire phylogeny of life on earth. - [Read more Tree of Life] |
| TREE-PUZZLE - http://www.tree-puzzle.de/ Tree-puzzle is a program that constructs phylogenetic trees from sequence alignments using the maximum likelihood method. - [Read more TREE-PUZZLE] |
| TreeJuxtaposer - http://olduvai.sourceforge.net/ TreeJuxtaposer is a free software tool that allows a visual comparison of two trees in Newick format (phylogenies, taxonomies, gene trees, etc.). It can work with trees having up to 500,000 nodes, and automatically calculates and marks the differences. - [Read more TreeJuxtaposer] |
| TreeView - http://taxonomy.zoology.gla.ac.uk/rod/treeview.html Generates nice graphics of trees; reads multiple tree file formats; available for download to Mac or PC. - [Read more TreeView] |
| UCMP Phylogeny Wing - http://www.ucmp.berkeley.edu/exhibit/phylogeny.html "Phylogeny-Diversity of Life Through Time" is an on-line exhibit at the University of California Museum of Paleontology website. There is an introduction to phylogenetics and cladistics, and you can navigate through a very informative phylogenetic tree r - [Read more UCMP Phylogeny Wing] |
| Understanding Evolution - http://evolution.berkeley.edu/evosite/evohome.html fantastic site for teaching/understanding evolution - [Read more Understanding Evolution] |
| Weighbor - http://www.t10.lanl.gov/billb/weighbor/index.html 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. - [Read more Weighbor] |
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