results_ACT_Neff.out.
infile.
The results are written out to screen. The program also creates
the file results_sample_size.out, which shows the size of the MCMC sample.
Example
> java BambeInfile
Info about the MCMC simulation:
Length of the burn-in period= 10000
Length of the sampling period= 20000
Tree topologies are written out every 40 steps.
MCMC sample size= 500
resultsAllTopos.out.
The program reads in this file and
translates the topology strings
into integer labels.
A translation table
is created and written out to file
resultsStringToIntegerTranslator.out.
The posterior probabilities for the different
topologies are written out to file
results_histo.out,
which is subsequently analysed with MATLAB programs.
dna.dat, and writes out a
a window of specified length and starting position
into file dna.in.
While this Java class is part of the overall JAMBE
package, it can also be used as a standalone application.
To this end, create a file with the name
in.windowStartEnd, which contains
two integers specifying the first and the last position
of the window.
For example,
500 1000
writes out the 501 sites between position 500 and 1000 from the original alignment.
resultsAllTopos.out
is too big. The program SubsetSelection.java overcomes
this problem by thinning out the file
resultsAllTopos.out.
Click here
for further details.