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#BFCA 1.0.2# Bayes Factor Cluster Analysis (BFCA) is a test of congruence among calibration hypotheses to assist their filtering prior to molecular clock analysis. It is a heuristic method based on the comparison of pairwise calibrations hypotheses by Bayes factors that allows identifying sets of congruent calibrations.

##Download## Linux (source code)

Mac

Windows

##Installation (R package)## ####Requirements:####

R >=3.0, R packages snow and snowfall

###Common### Install snow and snowfall packages:

install.packages(c("snow", "snowfall"), dependencies=TRUE)

The following instructions assume that you downloaded the corresponding bfca file in your Downloads folder; replace username by your user name.

###Linux### Type in an R session:

install.packages("/home/username/Downloads/bfca_1.02.tar.gz", type="source")

###Mac OS X### To install the binary package (compiled in Snow Leopard 10.6.8), type in the R console:

install.packages("/Users/username/Downloads/bfca_1.02.tgz")

If you have the Developer Tools installed, it is perhaps better to use the source package (or if you have problems installing the binary version). Type in the R console:

install.packages("/Users/username/Downloads/bfca_1.02.tar.gz", type="source")

###Windows 7### Type in the R console (assuming that you downloaded the bfca zip file in your Downloads folder; replace username by your user name):

install.packages("C:\\Users\\username\\Downloads\\bfca_1.02.zip")


#BFCA tools 1.0.1#

BFCA tools are a set of Perl scripts to help in the generation of xml input files required for the multiple runs of BEAST and the posterior processing of log files.

##Installation## The only requirement is to have a Perl 5.8.x (or higher) interpreter installed. Most Linux distributions and Mac OS X have Perl installed by default. In Windows you can install any of the recommended distributions.

The scripts are distributed in a compressed tar file (bfca_tools_v1.01.tar.gz), so you will need to unpack and decompress them. On UNIX / UNIX-like environments execute:

tar xvfz bfca_tools_v1.tar.gz 

In Windows you can use a tool such as 7-zip to do it.



#Tutorial#

This is a tutorial to run a Bayes Factor Cluster Analysis to evaluate the congruence of five calibration hypotheses with a gene simulated under a very simple model (strict clock; HKY; no rate heterogeneity; equal nucleotide frequencies).

https://bitbucket.org/visoca/bfca/downloads/tutorial1.tar.gz

Updated