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README.md

MGRA

Version: 2.3.0 beta

Release date: 5 October 2015

Server' website: http://mgra.cblab.org/

Description

MGRA (Multiple Genome Rearrangements and Ancestors) - a tool for reconstruction of ancestral gene orders and the history of genome rearrangements for multiple input genomes.

Installation

See docs/INSTALL.md file.

Usage

See docs/USAGE.md file.

Authors

  • Pavel Avdeyev (The George Washington University, Washington, DC)
  • Nikita Kartashov (Academic University, St. Petersburg, Russia)
  • Shuai Jiang (University of South Carolina)
  • Max Alekseyev (The George Washington University, Washington, DC)

Citation

  • P. Avdeyev, S. Jiang, S. Aganezov, F. Hu, and M. A. Alekseyev. "Reconstruction of ancestral genomes in presence of gene gain and loss", 2016. (submitted)
  • M. A. Alekseyev and P. A. Pevzner. "Breakpoint Graphs and Ancestral Genome Reconstructions". Genome Research 19(5) (2009), pp. 943-957

Related publications

  • S. Jiang and M. A. Alekseyev. "Linearization of Median Genomes under DCJ". Proceedings of the 14th Workshop on Algorithms in Bioinformatics" (WABI 2014), Lecture Notes in Computer Science 8701 (2014), pp. 97-106

Contacts

You can send your feedback at Max Alekseyev maxal@gwu.edu

You also can report bugs or suggest features using issue tracker at GitHub https://github.com/ablab/mgra/issues

Acknowledgements

The work was supported by National Science Foundation under the grant No IIS-1253614.

We would like to thank:

  • Nadiya Sitdykova
  • Aleksey Gurevich (testing and some useful suggestions)

Licence

MGRA is distributed under GNU GPL v2 license, see LICENSE.

It also uses third-party librarires and programs:

  • Blossom V (see src/libs/blossom5/LICENSE.TXT), author Vladimir Kolmogorov

http://pub.ist.ac.at/~vnk/software.html#BLOSSOM5

  • Boost (Boost Software License)

http://www.boost.org