Diversity Maps Files

Diversity Maps 0.1.0 (October 26, 2011)
Copyright (C) Fedor Konovalov; licenced under GNU GPL

RELEASE NOTES
For instructions, see the README files in version folders.

Version 0.1.0:

Major release with a great deal of novel functionality.

1. ADDED: Spectral mode (experimental).
This is a new algorithm loosely based on a sliding window approach. Instead of comparing your genotypes to a pair of references, it provides a true all-vs-all analisys of diversity. Color patterns are generated in full RGB spectrum based on the similarity of haplotypes in chromosome regions across all the population. This mode provides three ways to initialize the coloring pattern: automatically by PCA (default), load from file, or assign random initial colors, the latter producing mostly grey background on which the unique haplotypes clearly stand out. 

2. ADDED: Lots of color manipulation options in Spectral mode.
You can modify hue, swap and invert channels, change their gamma and saturation -- to get the best-looking image for visual inspection or to present your data in a printed form.

3. The program now requires more Perl modules to run, but everything is still bundled in Standalone packages. Though, if you use Perl, I recommend to install the modules.


Version 0.0.3:

1. ADDED: Automatic reference selection. 
If no references are specified with -r1/-r2, it selects the pair of accessions with the largest genetic distance from each other (for example, in F2 population the parents will most probably be selected as references).
If only one reference is specified (either -r1 or -r2), the second reference is selected automatically.

2. ADDED: Single reference option.
With -rs <name>, you can choose to work with a single reference only.


Version 0.0.2:

First public release.