This project provides algorithms written in Scala which are used in the bioinformatics domain.
Highlights so far:
- generic (2D) dynamic programing algorithm (see
net.gumbix.dynpro.DynPro) - Global, semi-local and local pairwise alignment (see
net.gumbix.bioinf.string.alignment.Alignment) - Multiple alignment
- star algorithm, see
net.gumbix.bioinf.string.alignment.StarAlignment - Clustal variant, see
net.gumbix.bioinf.string.alignment.Clustal
- star algorithm, see
- Phylogenetic tree algorithms
- Neighbor-Joining, see
net.gumbix.bioinf.phylo.NeighborJoiningTree - Fitch-Margoliash, see
net.gumbix.bioinf.phylo.FitchMargoliashTree
- Neighbor-Joining, see
- Pattern recognition with the Viterbi-algorithm (hidden markov model, see
net.gumbix.bioinf.hmm.Viterbi) - RNA 2D struct viewer based on Nussinov algorithm (see
net.gumbix.bioinf.struct.RNAStruct2DViewer) - Greedy superstring algorithm for sequence assembly (see
net.gumbix.bioinf.string.seq.GreedySuperstring) - and many more...
The Maven module demo contains several examples.
More documentation will come soon. Please refer to project home page or the to the wiki pages for more information. A good start is to read the preliminary manual or the generated scaladoc API documentation. See installation below where to find it.
There are two important branches:
- master: The main branch that contains the sequential dynamic programming algorithm.
- conc_dp: An experimental branch that uses a concurrent dynamic programming approach.
The project uses Maven 3 as the build tool. Check out the project and run the Maven goal mvn site. This will generate all the relevant artifacts. The scaladoc can be found in ./target/site/index.html. More details are described int the manual.
None yet. :-)
The software was originally developed for a lecture on bioinformatics. Thus, this software was mainly supposed to be for academic use. However, I believe that part of it might be of common interest. Let's see how this project relates to Biojava and other projects like bioscala.