BEST Bayesian: Difference between revisions
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Latest revision as of 08:50, 26 February 2013
Category
Bioinformatics
Program On
zcluster
Version
2.3.1
Author / Distributor
Description
"BEST is a free phylogenetics program to estimate the joint posterior distribution of gene trees and species tree using multilocus molecular data that accounts for deep coalescence but not for other issues such as horizontal transfer or gene duplication." more at BEST
Running Program
This code works as a modification of the popular phylogenetics software package MrBayes
/usr/local/BEST/latest is pointed to the latest update versionat /usr/local/BEST/2.3.1
Example of interactive program. Please refer to Run interactive Jobs .
qlogin /usr/local/best/latest/best ... exit
Documentation
Online tutorial available at BEST
Commands that are available from the command line or from a MrBayes block include: About -- Describes the program Acknowledgments -- Shows program acknowledgments Charset -- Assigns a group of sites to a set Charstat -- Shows status of characters Citations -- Appropriate citation of program Comparetree -- Compares the trees from two tree files Constraint -- Defines a constraint on tree topology Ctype -- Assigns ordering for the characters Databreaks -- Defines nucleotide pairs (doublets) for stem models Delete -- Deletes taxa from the analysis Deroot -- Deroots user tree Disclaimer -- Describes program disclaimer Exclude -- Excludes sites from the analysis Execute -- Executes a file Help -- Provides detailed description of commands Include -- Includes sites Link -- Links parameters across character partitions Log -- Logs screen output to a file Lset -- Sets the parameters of the likelihood model Manual -- Prints a command reference to a text file Mcmc -- Starts Markov chain Monte Carlo analysis Mcmcp -- Sets the parameters of a chain (without starting analysis) Outgroup -- Changes outgroup taxon Pairs -- Defines nucleotide pairs (doublets) for stem models Partition -- Assigns a character partition Plot -- Plots parameters from MCMC analysis Prset -- Sets the priors for the parameters Props -- Set proposal probabilities Quit -- Quits the program Report -- Controls how model parameters are reported Restore -- Restores taxa Root -- Roots user tree Set -- Sets run conditions and defines active data partition Showmatrix -- Shows current character matrix Showmodel -- Shows model settings Showtree -- Shows user tree Sump -- Summarizes parameters from MCMC analysis Sumt -- Summarizes trees from MCMC analysis Taxastat -- Shows status of taxa Taxset -- Assigns a group of taxa to a set Unlink -- Unlinks parameters across character partitions Usertree -- Defines a single user tree Version -- Shows program version Commands that should be in a NEXUS file (data block or trees block) include: Begin -- Denotes beginning of block in file Dimensions -- Defines size of character matrix End -- Denotes end of a block in file Endblock -- Alternative way of denoting end of a block Format -- Defines character format in data block Matrix -- Defines matrix of characters in data block Translate -- Defines alternative names for taxa Tree -- Defines a tree from MCMC analysis Note that this program supports the use of the shortest unambiguous spelling of the above commands (e.g., "exe" instead of "execute").
Installation
Source downloaded from BEST
System
64-bit Linux