RASP (Reconstruct Ancestral State in Phylogenies): A tool for historical biogeography

• Published in: Molecular phylogenetics and evolution Vol. 87; pp. 46 - 49
• Main Authors: Yu, Yan, Harris, A.J., Blair, Christopher, He, Xingjin
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.06.2015
• Subjects: Ancestral state reconstruction; Computer Graphics; Genetic Speciation; Historical biogeography; Models, Statistical; Phylogeny; Phylogeography; Sequence Analysis, DNA; Software; Uncertainty; User-Computer Interface; Historical biogeography; Ancestral state reconstruction; Software
• ISSN: 1055-7903; 1095-9513
• DOI: 10.1016/j.ympev.2015.03.008

[Display omitted] •We introduce software package RASP, which is a tool for historical biogeography.•We improve the widely used S-DIVA method, the DEC model, the Statistical DEC model and BayArea.•RASP also contains tools for combing the results from multiple runs and tools for removing widely distributed outgroups. We announce the release of Reconstruct Ancestral State in Phylogenies (RASP), a user-friendly software package for inferring historical biogeography through reconstructing ancestral geographic distributions on phylogenetic trees. RASP utilizes the widely used Statistical-Dispersal Vicariance Analysis (S-DIVA), the Dispersal–Extinction–Cladogenesis (DEC) model (Lagrange), a Statistical DEC model (S-DEC) and BayArea. It provides a graphical user interface (GUI) to specify a phylogenetic tree or set of trees and geographic distribution constraints, draws pie charts on the nodes of a phylogenetic tree to indicate levels of uncertainty, and generates high-quality exportable graphical results. RASP can run on both Windows and Mac OS X platforms. All documentation and source code for RASP is freely available at http://mnh.scu.edu.cn/soft/blog/RASP.