Genomic sequence analysis library and applications. Not intended to be used for large projects or lab projects. More like Ian's private/public C sandbox.
Building the software is as simple as:
make
This will build the genomikon library and the applications below. To perform some functional tests, you can:
make test
The testing program in the main directory is used to check for memory leaks
and is not part of the functional tests.
There are several applications built with the genomikon library. Each of these has its own directory.
- dusty - a complexity filter for nucleotide sequences
- isoformer - programs for generating alternative splicing isoforms
- hmmstar - a viterbi decoder for nucleotide sequences and k-mer models
- presti - an HMM for classifying integers (e.g. read coverage)
- smithy - a simple implementation of Smith-Waterman
- viterby - a simple Viterbi decoder for HMMs specified in JSON
- wordy - a word game that mixes boggle and genetic algorithms
Ian Korf