文档库

最新最全的文档下载
当前位置:文档库 > BEAST软件计算分化时间

BEAST软件计算分化时间

Relaxed Phylogenetics and Dating with Confidence

Alexei J Drummond and Andrew Rambaut

April 1,2010

Introduction

This practical will introduce the BEAST software for Bayesian evolutionary analysis,with a focus on estimating phylogenies and divergence

BEAST软件计算分化时间

times when you have calibration information from fossil evidence or other prior knowledge.

You will need the following software at your disposal:

•BEAST -this package contains the BEAST program,BEAUti,TreeAnnotator and other utility programs.This tutorial is written for BEAST v1.5.x,which has support for multiple partitions.It is available for download from

http://beast.bio.ed.ac.uk/.

•Tracer -this program is used to explore the output of BEAST (and other Bayesian MCMC programs).It graphically and quantitively summarizes the dis-tributions of continuous parameters and provides diagnostic information.At the time of writing,the current version is v1.5..It is available for download from http://beast.bio.ed.ac.uk/.

•FigTree -this is an application for displaying and printing molecular phylogenies,in particular those obtained using BEAST.At the time of writing,the current version is v1.3.1.It is available for download from http://tree.bio.ed.ac.uk/.Rates and dates

This tutorial will guide you through the analysis of an alignment of sequences sampled from twelve primate species.The goal is to estimate the phylogeny as well as the rate of evolution on each lineage based on dates of divergence of their host species.

The first step will be to convert a NEXUS file with a DATA or CHARACTERS into a BEAST XML input file.This is done using the program BEAUti (this stands for Bayesian Evolutionary Analysis Utility).This is a user-friendly for setting the evolutionary model and options for the MCMC analysis.The second step is to actually run BEAST using the input file that contains the data,model and settings.

1n. 刻度;校准;标度