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• Dr. Rasmus Nielsen Laboratory
  * [http://mrbayes.csit.fsu.edu/index.php MrBayes: Bayesian Inference of Phylogeny] — Official Homepage * [http://workshop.molecularevolution.org/resources/references/ Molecular Evolution papers]
  1 KB (147 words) - 15:39, 5 July 2012
• Phylogenetics
  ...the science of estimating the evolutionary past, in the case of molecular phylogeny, based on the comparison of DNA or protein sequences." — Sandra L. Ba ...cters observed in the species included, and are usually used for molecular phylogeny where the characters are aligned nucleotide or amino acid sequences.
  11 KB (1,505 words) - 18:58, 30 September 2006
• MrBayes
  '''MrBayes''' is a program for the Bayesian estimation of phylogeny. ...evolution.org/software/mrbayes/files/mrbayes_2004.pdf Bayesian Analysis of Molecular Evolution using MrBayes] — by Huelsenbeck JP and Ronquist F.
  3 KB (373 words) - 02:43, 13 July 2012
• Maximum parsimony
  ...eel M and Penny D (2000). Parsimony, likelihood, and the role of models in molecular phylogenetics. ''Molec Biol Evol'' '''17''':839-850. ...ive to parsimony for inferring phylogeny using nucleotide sequence data. ''Molecular Systematics of Plants II.'' Kluwer (Boston).
  6 KB (941 words) - 04:51, 13 September 2006
• Neighbour joining
  ...our-joining''' is a bottom-up clustering method used for the creation of [[phylogeny|phylogenetic]] [[tree data structure|tree]]s. Usually used for trees based ...hbour-joining does not assume that all lineages evolve at the same rate ([[molecular clock hypothesis]]) and produces an unrooted tree.
  2 KB (240 words) - 10:35, 19 April 2007
• Long branch attraction
  The most problematic and pervasive problem in molecular phylogeny is the problem of 'long branch attraction' (Felsenstein, 1978; Gribaldo and * Baldauf SL (2003). Phylogeny for the faint of heart: a tutorial. ''TRENDS in Genetics'' '''19(6)''':345-
  3 KB (371 words) - 04:51, 13 September 2006
• UPGMA
  ...used in [[:Category:Bioinformatics|bioinformatics]] for the creation of [[phylogeny|phylogenetic]] trees. ...od for inferring phylogenetic trees unless the constant-rate assumption ([[molecular clock hypothesis]]) has been tested and justified for the data set being us
  2 KB (327 words) - 10:34, 19 April 2007
• Bootstrapping
  * Bootstrapping does not correct biases in phylogeny methods * Baldauf SL (2003). Phylogeny for the faint of heart: a tutorial. ''TRENDS in Genetics'' '''19(6)''':345-
  5 KB (732 words) - 04:52, 13 September 2006
• Inferring Phylogenies
  <li>Perfect phylogeny</li> <li>Does a molecular clock guarantee consistency?</li>
  20 KB (3,034 words) - 10:55, 6 January 2006
• List of EMBOSS programs
  ;fdnaml : Estimates nucleotide phylogeny by maximum likelihood ;fdnamlk : Estimates nucleotide phylogeny by maximum likelihood
  21 KB (2,762 words) - 01:04, 10 July 2012