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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 |

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