Deambulum Analyse - Phylogénie Le Deambulum : Analyse Phylogénie CIPRes Building the Tree of Life: A National Resource for Phyloinformatics and Computational Phylogenetics. (Harvard University Herbaria, and the University of California, Davis, US) TreeBASE - A Database of Phylogenetic Knowledge TreeBASE stores phylogenetic trees and the data matrices used to generate them from published research papers. Search Tree of Life web project Package PHYLIP (Phylogeny Inference Package, Joe Felsenstein, Department of Genetics at the University of Washington) Documentation à Infobiogen Individual program documentations Main documentation Tutorials for PHYLIP (BIRCH, Bioinformatics Resources, University of Manitoba, Canada) Phylogenetic analysis using parsimony Phylogenetic analysis discrete state data Phylogenetic analysis using distance methods BABEL (Infobiogen) Emboss via Babel Programmes Phylip Bioweb : Phylogénie (Institut Pasteur) Programmes Phylip fastDNAml Construction of phylogenetic trees of DNA sequences using maximum likelihood Bioportal (BIC, National University of Singapore) WebPhylip Phylip programs for molecular sequence analysis BCF (Bioinformatics Core Facility) Center for Biotechnology, University of Nebraska-Lincoln) WebPhylip web version of the original PHYLIP package Bioinformatics Toolkit (CMBI, University of Nijmegen) DrawTree - DrawGram Bioweb : Phylogénie (Institut Pasteur) Phylip fastDNAml BIONJ A version of the NJ algorithm improved for molecular sequences. Documentation Molphy Analyses phylogénétiques par les méthodes de maximum de vraisemblance (ML: maximum likelihood) et Neighbor-joining. (ProtML, NucML, ProtST, NJDist) Njdist NJDist Neighbor Joining Phylogeny from Distance Matrix PUZZLE Tree reconstruction for sequences by quartet puzzling and maximum likelihood. Documentation SeqGen Sequence-Generator. Documentation treealign A Unified Approach to Alignments and Phylogenies. It uses a combination of distance matrix and approximate parsimony methods. Pyramids A pyramidal analysis tool for sequence clustering. Documentation QR2 A reduction algorithm for approximating a (nonmetric) dissimilarity by a tree distance Documentation PHYLOQUART A collection of programs aimed at estimating phylogenies from a quartet principle. The idea is to proceed in two steps: i) every set of four species is considered and one (or none) of the three possible bifuracting trees is chosen; ii) the 'quartets' (or trees on four species) are combined in an overall tree on the entire set of species. Documentation LVB Reconstructing Evolution With Parsimony And Simulated Annealing. Documentation BAMBE : Bayesian Analysis in Molecular Biology and Evolution (Simon & Larget) TipDate Analysis of trees with dated tips. A program to estimate the rate of molecular evolution and time-scale of a phylogeny from dated sequences. Weighbor Weighted neighbor joining. Documentation DRUID Localization of recombination breakpoints in an alignment of sequences filtersites Filter conserved sites in an alignment. QuickTree Rapid reconstruction of phylogenies by the Neighbor-Joining method. GeneBee services (Belozersky Institute, Université de Moscou) TreeTop Phylogenetic Tree prediction Graphical Phylogenetic Trees (Via clustalw) IUBio-Archive (Indiana University) Phylodendron Phylogenetic tree drawing Phylodendron Web form Représentation graphique d'arbres phylogénétiques. Services Offered by The CBRG (Computational Biochemistry Research Group, ETH, Zurich) AllAll Related peptide sequences (Trees, ancestral seq., MSA, predictions etc). A partir d'un ensemble de peptides voisins, AllAll (all-against-all matching) détermine les relations entre chacun de ces peptides et utilise ces résultats pour construire et calculer les arbres phylogénétiques, l'alignement multiple et la séquence ancestrale probable, ainsi que la prédiction de conformation de ces protéines en fonction de la conservation de certains patterns. TreeGen : Tree generation from distance data Phylogenetic Tree: Distance or Parsimony Trees from Sequences Evolutionary Analysis DARWIN (Data Analysis and Retrieval With Indexed Nucleotide/peptide sequences.). Interactive tool for peptide and nucleotide sequence analysis. (Software to download). Outil intégré proposant une recherche de répétitions, de patterns, la génération de séquences aléatoires et mutations, des alignements multiples et arbres phylogénétiques (etc ...) et commande à partir d'un langage de programmation propre. Evolutionary Relationships (BiBiServ, Universität Bielefeld, Allemagne) Splits Tree 2 Analyzing and Visualizing Evolutionary Data.

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