=====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://www.microbesonline.org/fasttree/|fasttree]] A alternative approach to RAxML. Much (much) faster, (marginally) less accurate?
  *ape (R package)
  *[[http://mrbayes.sourceforge.net/|MrBayes]] A Bayesian approach to phylogenetic analyses. Much (much) slower, more accurate (?), phylogenetics analyses come with estimates of posterior distribution of model parameters. 
  *[[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://tree.bio.ed.ac.uk/software/figtree/|Figtree]] Graphical viewer of phylogenetic trees
  *[[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://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.