Phylogenetic Trees

Alphabetical     Date
Phylogenetic Analysis with the iPlant Discovery Environment
Naim Matasci, Naim Matasci, Sheldon McKay, Sheldon McKay
Published online: June 2013
Detecting the Signatures of Adaptive Evolution in Protein‐Coding Genes
Joseph P. Bielawski
Published online: January 2013
Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities
Justin Kuczynski, Jesse Stombaugh, William Anton Walters, Antonio González, J. Gregory Caporaso, Rob Knight
Published online: November 2012
Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities
Justin Kuczynski, Jesse Stombaugh, William Anton Walters, Antonio González, J. Gregory Caporaso, Rob Knight
Published online: December 2011
Phylogenetic Analysis of Protein Sequence Data Using the Randomized Axelerated Maximum Likelihood (RAXML) Program
Antonis Rokas
Published online: October 2011
Using OrthoMCL to Assign Proteins to OrthoMCL‐DB Groups or to Cluster Proteomes Into New Ortholog Groups
Steve Fischer, Steve Fischer, Brian P. Brunk, Brian P. Brunk, Feng Chen, Xin Gao, Xin Gao, Omar S. Harb, Omar S. Harb, John B. Iodice, John B. Iodice, Dhanasekaran Shanmugam, David S. Roos, Christian J. Stoeckert, Christian J. Stoeckert
Published online: September 2011
Inferring Protein Function from Homology Using the Princeton Protein Orthology Database (P‐POD)
Michael S. Livstone, Rose Oughtred, Sven Heinicke, Benjamin Vernot, Benjamin Vernot, Curtis Huttenhower, Dannie Durand, Dannie Durand, Kara Dolinski
Published online: March 2011
Beyond Simple Homology Searches: Multiple Sequence Alignments and Phylogenetic Trees
Rebecca A. Zufall
Published online: June 2009
Maximum‐Likelihood Analysis Using TREE‐PUZZLE
Heiko A. Schmidt, Arndt von Haeseler
Published online: March 2007
Installing and Configuring CMap
Ben Faga
Published online: March 2007
Getting a Tree Fast: Neighbor Joining, FastME, and Distance‐Based Methods
Richard Desper, Olivier Gascuel
Published online: October 2006
Phylogenomic Inference of Protein Molecular Function
Nandini Krishnamurthy, Kimmen Sjölander
Published online: October 2005
Using PEBBLE for the Evolutionary Analysis of Serially Sampled Molecular Sequences
Matthew Goode, Allen G. Rodrigo
Published online: May 2004
What If I Don't Have a Tree?: Split Decomposition and Related Models
Daniel H. Huson
Published online: May 2003
Inferring Evolutionary Trees with PAUP*
James C. Wilgenbusch, David Swofford
Published online: February 2003
Using MODELTEST and PAUP* to Select a Model of Nucleotide Substitution
David Posada
Published online: February 2003
Visualizing Phylogenetic Trees Using TreeView
Roderic D.M. Page
Published online: August 2002