BEST Bayesian: Difference between revisions
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=== Category === | === Category === | ||
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=== Description === | === 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 [http://www.stat.osu.edu/~dkp/BEST/introduction/ BEST] | |||
[http://www.stat.osu.edu/~dkp/BEST/ | |||
=== Running Program === | === Running Program === | ||
This code works as a modification of the popular phylogenetics software package [[MrBayes]] | 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 [[Running_Jobs_on_zcluster#Running_an_Interactive_Job | Run interactive Jobs]] . | |||
<pre class="gcommand"> | |||
<pre class=" | |||
qlogin | qlogin | ||
/usr/local/best/latest/best | |||
... | ... | ||
exit | exit | ||
</pre> | </pre> | ||
=== Documentation === | === Documentation === | ||
Online tutorial available at [http://www.stat.osu.edu/~dkp/BEST/ | Online tutorial available at [http://www.stat.osu.edu/~dkp/BEST/introduction/ BEST] | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
Commands that are available from the command | Commands that are available from the command | ||
| Line 164: | Line 101: | ||
=== Installation === | === Installation === | ||
Source downloaded from [http://www.stat.osu.edu/~dkp/BEST/ | Source downloaded from [http://www.stat.osu.edu/~dkp/BEST/introduction/ BEST] | ||
=== System === | === System === | ||
64-bit Linux | 64-bit Linux | ||
Latest revision as of 09:50, 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