FCP
The fragment classification package (FCP) provides the following classifiers for assigning query fragments to their source genome:
- Naive Bayes (NB): a composition-based, rank-specific classifier
- BLASTN: a homology-based, rank-specific classifier
- NB-BL: a hybrid, rank-specific classifier combining NB and BLASTN
- Epsilon-NB (epsilon-NB): a composition-based, rank-flexible classifier
- Lowest common ancestor (LCA): a homology-based, rank-flexible classifier
- LCA + epsilon-NB: a hybrid, rank-flexible classifier combining LCA and epsilon-NB
License
This software is released under the GNU General Public License v3.0.
Obtaining the Software
The FCP is available as a compressed zip file:
After downloading, uncompress the FCP file and follow the installation instruction in the README file. FCP has been tested under Linux and Windows 7.
Version History
- December 13, 2010: initial software release.
Contact Information
The FCP is in active development and we are interested in discussing all potential applications of this software. We encourage you to send us suggestions for new features. Suggestions, comments, and bug reports can be sent to Rob Beiko (beiko [at] cs.dal.ca). If reporting a bug, please provide as much information as possible and a simplified version of the data set which causes the bug. This will allow us to quickly resolve the issue.
Citing the FCP
If you find this software helpful in your research, please cite:
Parks, D.H., MacDonald, N.J., and Beiko, R.G. (2010). Classify short genomic fragments from unrepresented lineages using composition and homology. (Submitted to ISMB, 2011)
Funding
The development and deployment of this software has been supported by several organizations:
- Killam Trusts
- Genome Atlantic
- The Dalhousie Centre for Comparative Genomics and Evolutionary Bioinformatics, and the Tula Foundation
- The Dalhousie Faculty of Computer Science
