BDIST is an implementation of Robinson and Cavanaugh's baraminic distance method as detailed in their 1998 paper "A quantitative approach to baraminology with examples from the catarrhine primates" (CRSQ 34(4):196-208). For a description of the method and its application, please refer to their paper. BDIST is written by Todd Wood and described in the paper, "A baraminology tutorial with examples from the grasses (Poaceae)" (TJ, in preparation). Because BDIST is written in perl, it should be platform independent. New to perl? Try the Perl Mongers' site for beginners.
Using the Software. The program uses a very simplistic format for inputting data; an example follows:
freddie 0 {10} 1 12 0 1 {01}
velma 0 {01} 2 13 {12} 0 ?
scooby 1 0 2 12 1 1 1
shaggy 0 1 0 14 2 0 {01}
daphne 0 0 2 12 0 1 {23}
The first column includes the taxa names. The coding of characters is standard for Nexus format; each column is a character. Unknown character states are indicated by "?", variable character states for a single taxon are simply listed in {}. The format can be delimited by any white-space (spaces, tabs, etc.), but each taxon's characters are separated from the next taxon by a newline. If you create a data matrix in a spreadsheet then save it as "tab-delimited text," it will be in the proper format.
To run the program on a file called testfile, in a unix shell, type bdist.pl testfile. For Windows, type perl bdist.pl testfile at the MS-DOS prompt. The output will always be written to a file called bdist.txt, which should be viewable in any textviewer. The baraminic distance matrix will also be included in this file and can be cut and pasted to another file for further analysis.
Output. This is an example of the output of BDIST:
BDIST performs Baraminic Distance analyses on cladistic datasets.
version 1.0 October 3, 2001
Please cite:
Robinson, D.A. and D.P. Cavanaugh. 1998. A quantitative approach to
baraminology with examples from the primates. CRSQ 34:196-208.
Wood, T.C. 2001. BDIST software, v. 1.0. Center for Origins Research
and Education, Bryan College. Distributed by the author.
Input file: testfile
Date: Thu Oct 18 05:40:58 2001
Number of taxa: 5
Number of characters: 7
Character Relevance
--------- ---------
1 1.000
2 1.000
3 1.000
4 1.000
5 1.000
6 1.000
7 0.800
Characters with a<0.95: 1
6 characters will be used in the BDIST analysis
Character Diversity
--------- ---------
1 0.150
2 0.650
3 0.450
4 0.450
5 0.650
6 0.350
--------------------Distance Matrix--------------------
daphne freddie scooby shaggy velma
daphne 0.000 0.167 0.333 0.833 0.500
freddie 0.167 0.000 0.500 0.667 0.667
scooby 0.333 0.500 0.000 1.000 0.500
shaggy 0.833 0.667 1.000 0.000 0.333
velma 0.500 0.667 0.500 0.333 0.000
