Conrad engine

calhoun.analysis.crf	the interface, main Conrad class, and solver for the Conrad engine.
calhoun.analysis.crf.executables.viewer	prototype of a viewing utility for examiining the results of inference.
calhoun.analysis.crf.features.generic	features useful across different models
calhoun.analysis.crf.solver	training and inference algorithms used in the CRF engine

Conrad gene caller

calhoun.analysis.crf.features.interval13	mdoel definition and setup for the interval13 model
calhoun.analysis.crf.features.interval29
calhoun.analysis.crf.features.supporting	utility classes used by feature managers in gene calling models
calhoun.analysis.crf.features.supporting.phylogenetic	utility classes for phylogenetic analysis
calhoun.analysis.crf.features.tricycle13	basic features and model for the tricycle13 gene calling model
calhoun.analysis.crf.io	handles input and output of gene calling formats
calhoun.analysis.crf.scoring	local similarity functions used in gene calling models

Other Packages

calhoun.analysis.crf.solver.semimarkov
calhoun.analysis.crf.statistics	math utilities used by features and to evaluate results
calhoun.analysis.crf.test
calhoun.analysis.crf.test.slow
calhoun.seq
calhoun.seq.test
calhoun.util