Instructions for using sampler and searcher programs

The sampler program requires several additional files to be within the same directory or to be entered as input parameters. These include an annotation file, a file with list of genes, as well as several files that provide phylogenetic footprint information. These files are included here, and were generated as described in the text of the accompanying paper. They must be included in the same directory as the sampler program in order for the program to function properly. The files are:

Auxilliary modules to work in combination with sampler and searcher programs

C code for training program.
PERL code for script.

The training program can be run on any sequence comparisons in the AVID alignment format. It is used to generate the subsequence conservation profiles for phylogenetic footprints.

The random_selector script is a perl script that works together with the sampler program. This script randomly selects 1000 PFs for use in the ranking procedure important in the updating step.

For more information, please contact Yonatan Grad.

Last updated by YG on 20 January 2004.