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phylogenetics [2014/11/14 15:55] sebastien.renaut |
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| - | ===Phylogenetic analyses === | + | =====Phylogenetic analyses ===== |
| + | *See also [[http://qcbs.ca/wiki/buildingaphylogeny|this page]] on the blog with details about phylogenetic analyses | ||
| + | ===Computer programs === | ||
| *[[http://sco.h-its.org/exelixis/web/software/raxml/index.html|raxml]] A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies using Maximum Likelihood. | *[[http://sco.h-its.org/exelixis/web/software/raxml/index.html|raxml]] A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies using Maximum Likelihood. | ||
| *[[http://www.microbesonline.org/fasttree/|fasttree]] A alternative approach to RAxML. Much (much) faster, (marginally) less accurate? | *[[http://www.microbesonline.org/fasttree/|fasttree]] A alternative approach to RAxML. Much (much) faster, (marginally) less accurate? | ||
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| *[[http://phylo.bio.ku.edu/software/sate/sate.html|SATé - Simultaneous Alignment and Tree Estimation]] Software package for inferring a sequence alignment and phylogenetic tree. The iterative algorithm involves repeated alignment and tree searching operations. The original data set is divided into smaller subproblems by a tree-based decomposition. These subproblems are aligned and further merged for phylogenetic tree inference. | *[[http://phylo.bio.ku.edu/software/sate/sate.html|SATé - Simultaneous Alignment and Tree Estimation]] Software package for inferring a sequence alignment and phylogenetic tree. The iterative algorithm involves repeated alignment and tree searching operations. The original data set is divided into smaller subproblems by a tree-based decomposition. These subproblems are aligned and further merged for phylogenetic tree inference. | ||
| *[[http://evolution.genetics.washington.edu/phylip.html|Phylip]] Package of programs for inferring phylogenies. | *[[http://evolution.genetics.washington.edu/phylip.html|Phylip]] Package of programs for inferring phylogenies. | ||
| - | *figtree | + | *[[http://tree.bio.ed.ac.uk/software/figtree/|Figtree]] Graphical viewer of phylogenetic trees |
| - | *palm | + | *[[http://abacus.gene.ucl.ac.uk/software/paml.html|PAML]] Phylogenetic Analysis by Maximum Likelihood for protein and DNA sequences. Widely used to infer selection in specific species, tree branches, protein sequences (dn/ds). |
| *[[http://www.splitstree.org/|Splitstree4]] Application for computing unrooted phylogenetic networks from molecular sequence data. The nice GUI makes it a easy option for begineers. | *[[http://www.splitstree.org/|Splitstree4]] Application for computing unrooted phylogenetic networks from molecular sequence data. The nice GUI makes it a easy option for begineers. | ||
| - | *[[http://beast.bio.ed.ac.uk/|Beast]] Framework for testing evolutionary hypotheses, based on MCMC (i.e. bayesian). Divergence date and Molecular clock models. | + | *[[http://beast.bio.ed.ac.uk/|Beast]] Framework for testing evolutionary hypotheses, based on MCMC (i.e. bayesian). Divergence date and Molecular clock models. See more info on [[http://qcbs.ca/wiki/phylogeny_with_beast|this]] page. |
