Bayesian Application for Recombination and Gene Conversion Estimation

In UNIX, type the name of the executable program at the UNIX prompt and hit return. This will bring up the following menu:

Main Menu for MCMC-HMM
----------------------

1)	Model submenu
2)	Run settings submenu
3)	File submenu

Enter in a number to choose an option to change or enter Y if you're happy with the current options:

Type in a 3 and return to get to the file submenu. This shows you the default names of all the output files created by the program:

File containing the data	7	seq.phy
File for storing the settings	S	settings.out
File for storing lpd values	L	lpdfile.out
File for storing mean branch length	G	branch.out
File for storing the topology posterior probs	Z	topol_prob.out
File for storing the stationary frequency values	V	pi.out
File for storing the tstv ratio values	K	tstv.out

To change the name of a file, just choose the letter shown in the second column and type in a new name. The file seq.phy is the input file with the DNA sequence alignment, which has to be in sequential PHYLIP format. The program creates three further output files, whose names cannot be changed:

lambda.out	Evolution of the recombination parameter (the difficulty of changing tree topology)
ar.log	Evolution of the acceptance probability
tempfile	A temporary file that can be deleted

All output files are in ASCII format. The software package includes a MATLAB program to plot and display the results.

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Last modified: March 2002