Differences

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--- phylogenetics [2014/11/17 13:12]
sebastien.renaut
+++ phylogenetics [2014/12/02 16:13] (current)
sebastien.renaut
@@ Line 1: / Line 1: @@
-===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://www.microbesonline.org/fasttree/|fasttree]] A alternative approach to RAxML. Much (much) faster, (marginally) less accurate?
@@ Line 8: / Line 10: @@
   *[[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. One of the first and most commonly used program for phylogenetic analyses.
+  *[[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.
+  *[[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.