gDAM

gDAM is a Perl script to generate a graphical table representing data availability in a concatenated sequence alignment. It takes a concatenated alignment as input (nexus format) and generates a graphical table in the SVG (scalable vector graphics) format, which can be imported in most vectorial drawing software. Various data availability statistics are reported and added to the table. If desired, column and row headers are filled with a color indicating the amount of data available for that column or row.

Example output

Data availability matrix of a green algal multi-locus alignment (click to get PDF version).


Download

gDAM.pl v.1.01 download script and example alignment (.tar.gz)

Citation

If you find this software useful, please cite it in your work. I recommend citing it as follows:
Verbruggen H. (2011) gDAM: graphical Data Availability Matrix version 1.01. http://www.phycoweb.net/software

Notes and disclaimer

gDAM is in development and has not been tested extensively. It is quite plausible that incorrectly formatted input will lead to nonsensical output. In such cases, you should double-check your alignment, compare it to the example alignment and try again. If this still doesn't work, please feel free to write me an email (heroen.verbruggen@gmail.com).

gDAM is open-source and distributed according to the GNU General Public License. The program is provided "as is" without warranty of any kind, either expressed or implied. The entire risk as to the quality and performance of the program is with you. Should the program prove defective, you assume the cost of all necessary servicing, repair or correction. The author will not be liable to you for damages, including any general, special, incidental or consequential damages arising out of the use or inability to use the program (including but not limited to loss of data or data being rendered inaccurate or losses sustained by you or third parties or a failure of the program to operate with any other programs).

Dependencies and links

Before running the uncompiled scripts, make sure you have these Perl modules installed. They can be obtained from CPAN.

  • Graphics::ColorUtils
  • SVG
  • Links:

  • cpan: comprehensive perl archive network