Bayesian Application for Recombination and Gene Conversion Estimation

In UNIX, just type the name of the executable program at the UNIX pronpt and hit return. This will bring up the main 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:

This gives you the option between three submenus. Type 1 and you will get the model submenu:

Model Options
-------------

Model (JC+gaps, K2P+gaps, F81+gaps and F84+gaps)	M	F84
Estimate initial character frequencies from data	E	YES
Estimate transition/transversion ratio from data	R	YES
Frequencies of the three topologies	P	0.333333 0.333333 0.333333
Difficulty of changing trees	D	0.9
Read in initial hidden state sequence?	J	YES

Enter in a letter to choose an option to change or enter X to return to the main menu:

Select a letter to change the respective default option. For example, if you want to create the initial sequence of hidden states at random rather than read it in from file, type J. This toggles between YES and NO for this option:

Read in initial hidden state sequence?

J

YES

This reads in the initial hidden state sequence from file mosaic.in.

Read in initial hidden state sequence?

J

NO

This generates a random initial sequence of hidden states.

Or if you want to change the recombination parameter (the difficulty of changing trees), type D followed by the new value. When you are done, type X to go back to the main menu, and then select 2. This gives you the run settings submenu:

Run settings menu
-----------------

Length of the burn-in period	B	100000
Length of the sampling period	.	100000
Number of points to return	N	1000
Thinning interval	I	100
Tuning interval (for proposal distributions)	C	100
Update lambda with Gibbs sampling	W	YES
Annealing scheme for lambda	Q	PAR
Update stationary frequencies in MCMC algorithm	U	YES
Update transition-transversion ratio in MCMC algorithm	A	YES
Branch length in initial trees	O	0.1

Enter in a letter to choose an option to change or enter X to return to the main menu:

Again, select a letter to change the respective default option. For example, the default option for the annealing scheme is PAR:

Annealing scheme for lambda	Q	PAR

This gives annealing by mixing parameters . Type Q and you get:

Annealing scheme for lambda	Q	PROB

This gives annealing by mixing distributions . Typing Q again gives

Annealing scheme for lambda	Q	NONE

in which case no annealing is performed.

When you are done, type X to go back to the main menu. If you want to change the names of the output files, select 3. Otherwise, type X to go back to the main menu, and type Y to start the program.

Back to the main page of the manual.
Last modified: March 2002