Bifurcator by Ben Fry | Download Revision 21

This application creates a bifurcation plot from a set of
haplotype data. Given a set of SNPs that define a "core"
region, a tree is produced that shows how the genotypes of
a set of individuals bifurcate and differentiate themselves
from that point.

usage: [--actual-positions] [--less-text]
       <phased_file> <position_file>
       <core_position> <core_length>
       <left_branch_length> <right_branch_length> <font_size>

Example: java -jar bifurcator.jar ceph3.phase ceph3.pos 32 1 10 10 5
(the download includes the input files for this example)

--actual-positions  will horizontally place SNPs based on
                    genomic position instead of equidistant

--less-text         this options shuts of text for anything
                    except for the core region.

The <phased_file> parameter should be a file that contains
phased haplotype data. The first two columns of the data
are ignored. Additional columns are expected to contain
1, 2, 3, or 4 to signify A, C, G, or T.

The <position_file> parameter should specify a file that
lists the position of each SNP on its own line.

If you use this software for publication, please send a note
with the reference or a link. When citing this software, use:
Fry, B. Computational Information Design.
Ph.D. Thesis, Massachusetts Institute of Technology, (2004).

Bifurcator r21, released 1 October 2006
(c) Ben Fry (mail at benfry dot com)