Phylogenetic Analysis with the iPlant Discovery Environment. Issue 1 (1st June 2013)

• Record Type: Journal Article
• Authors: Matasci, Naim; McKay, Sheldon
• Editors: Baxevanis, Andreas D.; Petsko, Gregory A.; Stein, Lincoln D.; Stormo, Gary D.
• Is Part Of: Current protocols in bioinformatics. Volume 42:Issue 1(2013)
• Page Start: 6.13.1
• Page End: 6.13.13
• Publication Date: 2013-06-01
• Subjects: phylogenetics -- maximum likelihood -- continuous ancestral character estimation -- multiple sequence alignment; Bioinformatics -- Laboratory manuals; Nucleotide sequence -- Laboratory manuals; Amino acid sequence -- Laboratory manuals; Base Sequence; Amino Acid Sequence; Computational Biology -- methods; Databases, Genetic; Proteins -- analysis; Sequence Analysis -- methods; Sequence Homology; Amino acid sequence; Bioinformatics; Nucleotide sequence; Laboratory Manuals; Laboratory manuals; 570.285
• DOI: 10.1002/0471250953.bi0613s42
• Languages: English
• ISSNs: 1934-3396

Abstract

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. Curr. Protoc. Bioinform . 42:6.13.1‐6.13.13. © 2013 by John Wiley & Sons, Inc.