beast软件linux用法,关于BEAST的使用1

BEAST v1.6.0 2002-2010

Bayesian Evolutionary Analysis Sampling

Trees

by

Alexei J. Drummond, Andrew Rambaut & Marc

Suchard

Department of Computer

Science

University of

Auckland

[e-mail]

Institute of Evolutionary Biology

University of Edinburgh

[e-mail]

David Geffen School of

Medicine

University

of California, Los Angeles

[e-mail]

Last updated: [e-mail] - 1st September

2010

Contents:

1) INTRODUCTION

2) INSTALLING BEAST

3) CONVERTING SEQUENCES

4) RUNNING BEAST

5) ANALYZING RESULTS

6) NATIVE LIBRARIES

7) SUPPORT & LINKS

8) ACKNOWLEDGMENTS

___________________________________________________________________________

1) INTRODUCTION

BEAST (Bayesian evolutionary analysis sampling trees) is

package for

evolutionary inference from molecular

sequences.

BEAST uses a complex and powerful input format (specified

in XML) to

describe the evolutionary model. This has advantages in

terms of

flexibility in that the developers of BEAST do not have to

try and predict

every analysis that researchers may wish to perform and

explicitly provide

an option for doing it. However, this flexibility means it

is possible to

construct models that don't perform well under the Markov

chain Monte Carlo

(MCMC) inference framework used. We cannot test every

possible model that

can be used in BEAST. There are two solutions to this:

Firstly, we  supply

a range of recipes for commonly performed analyses that we

know should work

in BEAST and provide example input files for these

(although, the actual

data can also produce unexpected behavour). Secondly, we

provide advice and

tools for the diagnosis of problems and suggestions on how

to fix them:

BEAST is not a black-box into which you can put your data

and expect an

easily interpretable answer. It requires careful

inspection of the output

to check that it has performed correctly and usually will

need tweaking,

adjustment and a number of runs to get a valid answer.

Sorry.

___________________________________________________________________________

2) INSTALLING BEAST

BEAST requires a Java Virtual Machine to run. Many systems

will already

have this installed. It requires at least version 1.5 of

Java to run. The

latest versions of Java can be downloaded from:

If in doubt type "java -version" to see what version of

java is installed

(or if it is installed at all).

Mac OS X will already have a suitable version of Java

installed.

Within the BEAST.v1.6.x package will be the following

directories:

Directory

Contents

doc/

documentation of BEAST

examples/

some example NEXUS and XML files

lib/

Java & native libraries used by

BEAST

native/

some C code to compile into

native libraries

bin/

Scripts of the corresponding OS

___________________________________________________________________________

3) CONVERTING SEQUENCES

A program called "BEAUti" will import data in NEXUS

format, allow you to

select various models and options and generate an XML file

ready for use in

BEAST.

To run BEAUti simply double-click the "BEAUti v1.6.x.exe"

file in the BEAST

folder. If this doesn't work then you may not have Java

installed correctly.

Try opening an MS-DOS window and typing:

java -jar lib/beauti.jar

See also the separate BEAUti README.txt

document.

__________________________________________________________________________

4) RUNNING BEAST

To run BEAST simply double-click the "BEAST v1.6.x.exe"

file in the BEAST

folder. You will be asked to select a BEAST XML input

file.

Alternatively open a Command window and type:

java -jar lib/beast.jar input.xml

Where "input.xml" is the name of a BEAST XML format file.

This file can

either be created from scratch using a text editor or be

created by the

BEAUti program from a NEXUS format

file.

For documentation on creating and tuning the input files

look at the

documentation and tutorials on-line at:

Help -

FAQ -

Tutorials -

The latest manual can be downloaded from here:

BEAST arguments:

-verbose

"Give verbose XML parsing

messages"

-warnings

"Show warning messages about BEAST XML

file"

-strict

"Fail on non-conforming BEAST

XML file"

-window

"Provide a console

window"

-options

"Display an options

dialog"

-working

"Change working directory to

input file's directory"

-seed

"Specify a

random number generator seed"

-prefix

"PREFIX", "Specify a prefix

for all output log filenames"

-overwrite

"Allow overwriting of log files"

-errors

"Specify maximum number of

numerical errors before stopping"

-threads

"The number of computational

threads to use (default auto)"

-java

"Use Java

only, no native implementations"

-beagle

"Use beagle library if

available"

-beagle_info

"BEAGLE: show information on available

resources"

-beagle_order

"BEAGLE:

set order of resource use"

-beagle_instances

"BEAGLE: divide site patterns amongst

instances"

-beagle_CPU

"BEAGLE:

use CPU instance"

-beagle_GPU

"BEAGLE:

use GPU instance if available"

-beagle_SSE

"BEAGLE:

use SSE extensions if available"

-beagle_single

"BEAGLE:

use single precision if available"

-beagle_double

"BEAGLE:

use double precision if available"

-beagle_scaling

"BEAGLE: specify scaling

scheme to use"

-help"

"Print this

information and stop"

For example:

java -jar lib/beast.jar -seed 123456 -overwrite

input.xml

___________________________________________________________________________

5) ANALYZING RESULTS

We have produced a powerful graphical program for

analysing MCMC log files

(it can also analyse output from MrBayes and other MCMCs).

This is called

'Tracer' and is available from the Tracer web

site:

We have now included the "loganalyser" program again in

order to analyse

log and tree files without the need for tracer.

Additionally, two new programs are distributed as part of

the BEAST

package: LogCombiner & TreeAnnotator.

LogCombiner can combine log or tree

files from multiple runs of BEAST into a single combined

results file

(after removing appropriate burn-ins). TreeAnnotator can

summarize a sample

of trees from BEAST using a single target tree, annotating

it with

posterior probabilities, HPD node heights and rates. This

tree can then be

viewed in a new program called 'FigTree' which is

available from:

___________________________________________________________________________

6) NATIVE LIBRARIES

Some of the core of the BEAST program has been converted

into 'C' and can

be compiled into native code. This involves compiling the

source code in

'/native' into a shared library that Java can find and

use. We have

compiled this library for Mac OS X, Windows and Linux on

x86 machines. BEAST

should automatically find these libraries and use them. If

a suitable version

of this library is not found then BEAST will use a Java

version of the core

which will be slower.

___________________________________________________________________________

7) SUPPORT & LINKS

BEAST is an extremely complex program and as such will

inevitably have

bugs. Please email us to discuss any problems:

We would encourage you to join the BEAST users'

mailing-list to get

notifications of updates and bugs. At a later date this

may be expanded to

be a discussion-list so that users can exchange ideas and

help. You can

join the mailing list here:

The website for beast is here:

Source code distributed under the GNU Lesser General

Public License:

___________________________________________________________________________

8) ACKNOWLEDGMENTS

Thanks to the following for supplying code or assisting

with the creation

or testing of BEAST:

Alex Alekseyenko, Beth Shapiro, Chieh-Hsi Wu, Erik

Bloomquist,

Gerton Lunter, Joseph Heled, Korbinian Strimmer, Michael Defoin

Platel,

Oliver Pybus, Philippe Lemey, Roald Forsberg, Sebastian

Hoehna,

Sidney Markowitz, Simon Ho, Tulio de Oliveira, Oliver Pybus,

Vladimir Minin, Wai Lok Sibon Li, Walter Xie

+ numerous other users who have kindly helped make BEAST

better.