title: Phylogenetic analysis with the iPlant discovery environment.
abstract: The iPlant Collaborative's Discovery Environment is a unified Web portal to many bioinformatics applications and analytical workflows, including various methods of phylogenetic analysis. This unit describes example protocols for phylogenetic analyses, starting at sequence retrieval from the GenBank sequence database, through to multiple sequence alignment inference and visualization of phylogenetic trees. Methods for extracting smaller sub-trees from very large phylogenies, and the comparative method of continuous ancestral character state reconstruction based on observed morphology of extant species related to their phylogenetic relationships, are also presented.
authors.affiliation: The iPlant Collaborative.|The University of Arizona, Tucson, Arizona.
authors.forename: Naim
authors.initials: N
authors.lastname: Matasci
authors.affiliation: The iPlant Collaborative.|Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.
authors.forename: Sheldon
authors.initials: S
authors.lastname: McKay
mesh_terms: D029745:Codonopsis / Q000145:classification / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D030561:Databases, Nucleic Acid; D020407:Internet; D010802:Phylogeny; D016415:Sequence Alignment; D012984:Software