Software

BloDec

Description

BloDec is a program written in Java which computes the cutpoints of a finite metric space as described in [1]. In addition, the program can also compute the decomposition of the given metric into block metrics induced by the cutpoints.

Availability

BloDec and its source code are freely available under the GNU General Public License. To get the program, download the zipped folder from here. More information on how to use the program can be found in the README file which is also included in the zipped folder.

Contact

If you have questions concerning the program or would like to report a bug please contact me by e-mail.

Acknowledgments

This work has been supported in part by The British Council and the DAAD, within the ARC Programme.

Disclaimer

This program is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose.  See the GNU General Public License for more details.

Changes log

  • 19 April 2011: Bug in method for scaling output fixed.

References

  1. An algorithm for computing cutpoints in finite metric spaces. Andreas Dress, Katharina Huber, Jacobus Koolen, Vincent Moulton, Andreas Spillner. Journal of Classification, 27 (2), 158-192, 2010.

SuperQ

Description

SuperQ is a program written in Java which computes a phylogenetic super network from a collection of partial phylogenetic trees as described in [1] . The official website of the program is located at the University of East Anglia.

References

  1. SuperQ: computing supernetworks from quartets. Stefan Grünewald, Andreas Spillner, Sarah Bastkowski, Anja Bögershausen, Vincent Moulton. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10 (1), 151-160, 2013.

FlatNJ

Description

FlatNJ (FlatNetJoining) is a program written in Java for computing split networks that allow for interior vertices to be labeled while being (almost) planar as described in [1]. The official website of the program is located at the University of East Anglia.

References

  1. FlatNJ: A novel network-based approach to visualize evolutionary and biogeographical relationships. Monika Balvociute, Andreas Spillner, Vincent Moulton. Systematic Biology, 63 (3), 383-396, 2014.

SPECTRE

Description

SPECTRE is a suite of tools for inferring evolutionary patterns associated with reticulate evolution. More information can be found in the documentation.