├── .gitignore ├── .travis.yml ├── COPYING ├── MANIFEST.in ├── Makefile ├── README.rst ├── doc ├── .gitignore ├── Makefile ├── _static │ └── .gitignore ├── _templates │ └── .gitignore ├── commit-to-gh-pages.sh ├── conf.py ├── hash-tree.py ├── index.rst ├── intro.rst └── reference.rst ├── examples ├── conll.py └── nerdata │ ├── 000010470_mpeg21_p002.bio │ ├── 000010472_mpeg21_p002.bio │ ├── 000010472_mpeg21_p003.bio │ ├── 000010472_mpeg21_p004.bio │ ├── 000010472_mpeg21_p006.bio │ ├── 000010474_mpeg21_p002.bio │ ├── 000011329_mpeg21_p002.bio │ ├── 000014128_mpeg21_p001.bio │ ├── 000014128_mpeg21_p002.bio │ ├── 000014177_mpeg21_p001.bio │ ├── 000014177_mpeg21_p002.bio │ ├── 000014177_mpeg21_p003.bio │ ├── 000014177_mpeg21_p004.bio │ ├── 000014177_mpeg21_p005.bio │ ├── 000014177_mpeg21_p006.bio │ ├── 000014183_mpeg21_p003.bio │ ├── 000014241_mpeg21_p001.bio │ ├── 000014241_mpeg21_p002.bio │ ├── 000014241_mpeg21_p003.bio │ ├── 000014241_mpeg21_p004.bio │ ├── 000014241_mpeg21_p005.bio │ ├── 000014241_mpeg21_p006.bio │ ├── 000015594_mpeg21_p001.bio │ ├── 000015594_mpeg21_p002.bio │ ├── 000015594_mpeg21_p003.bio │ ├── 000015594_mpeg21_p004.bio │ ├── 000015594_mpeg21_p005.bio │ ├── 000015594_mpeg21_p006.bio │ ├── 000015594_mpeg21_p007.bio │ ├── 000015594_mpeg21_p008.bio │ ├── 000015594_mpeg21_p009.bio │ ├── 000015594_mpeg21_p010.bio │ ├── 000015594_mpeg21_p011.bio │ ├── 000015594_mpeg21_p012.bio │ ├── 000015594_mpeg21_p013.bio │ ├── 000015594_mpeg21_p014.bio │ ├── 000015594_mpeg21_p015.bio │ ├── 000015594_mpeg21_p016.bio │ ├── 000015594_mpeg21_p017.bio │ ├── 000015594_mpeg21_p018.bio │ ├── 000015594_mpeg21_p019.bio │ ├── 000015594_mpeg21_p020.bio │ ├── 000015800_mpeg21_p006.bio │ ├── 000015813_mpeg21_p002.bio │ ├── 000015815_mpeg21_p001.bio │ ├── 000015815_mpeg21_p002.bio │ ├── 000015815_mpeg21_p003.bio │ ├── 000015815_mpeg21_p004.bio │ ├── 000015815_mpeg21_p005.bio │ ├── 000015815_mpeg21_p006.bio │ ├── 000015815_mpeg21_p007.bio │ ├── 000015815_mpeg21_p008.bio │ ├── 000018165_mpeg21_p001.bio │ ├── 000018165_mpeg21_p002.bio │ ├── 000018165_mpeg21_p003.bio │ ├── 000018165_mpeg21_p004.bio │ ├── 000018165_mpeg21_p005.bio │ ├── 000018165_mpeg21_p006.bio │ ├── 000018165_mpeg21_p007.bio │ ├── 000018165_mpeg21_p008.bio │ ├── 000018165_mpeg21_p009.bio │ ├── 000018165_mpeg21_p010.bio │ ├── 000023647_mpeg21_p003.bio │ ├── 000023649_mpeg21_p001.bio │ ├── 000023649_mpeg21_p002.bio │ ├── 000023649_mpeg21_p003.bio │ ├── 000023649_mpeg21_p004.bio │ ├── 000023650_mpeg21_p001.bio │ ├── 000023650_mpeg21_p002.bio │ ├── 000023650_mpeg21_p003.bio │ ├── 000023650_mpeg21_p004.bio │ ├── 000023651_mpeg21_p001.bio │ ├── 000023651_mpeg21_p003.bio │ ├── 000023652_mpeg21_p001.bio │ ├── 000023653_mpeg21_p001.bio │ ├── 000023653_mpeg21_p002.bio │ ├── 000023653_mpeg21_p003.bio │ ├── 000023653_mpeg21_p004.bio │ ├── 000023658_mpeg21_p003.bio │ ├── 000023659_mpeg21_p001.bio │ ├── 000023659_mpeg21_p002.bio │ ├── 000023659_mpeg21_p003.bio │ ├── 000023659_mpeg21_p004.bio │ ├── 000023661_mpeg21_p001.bio │ ├── 000023661_mpeg21_p002.bio │ ├── 000023661_mpeg21_p003.bio │ ├── 000023661_mpeg21_p004.bio │ ├── 000023662_mpeg21_p001.bio │ ├── 000023662_mpeg21_p002.bio │ ├── 000023662_mpeg21_p003.bio │ ├── 000023662_mpeg21_p004.bio │ ├── 000023664_mpeg21_p003.bio │ ├── 000023666_mpeg21_p001.bio │ ├── 000023666_mpeg21_p002.bio │ ├── 000023666_mpeg21_p003.bio │ ├── 000023666_mpeg21_p004.bio │ ├── 000023667_mpeg21_p001.bio │ ├── 000023667_mpeg21_p002.bio │ ├── 000023667_mpeg21_p003.bio │ └── README ├── seqlearn ├── __init__.py ├── _decode │ ├── __init__.py │ ├── bestfirst.pyx │ ├── tests │ │ └── test_decode.py │ └── viterbi.pyx ├── _utils │ ├── __init__.py │ ├── ctrans.pyx │ ├── safeadd.pyx │ ├── tests │ │ ├── test_safeadd.py │ │ ├── test_transmatrix.py │ │ └── test_utils.py │ └── transmatrix.py ├── _version.py ├── base.py ├── datasets.py ├── evaluation.py ├── hmm.py ├── perceptron.py └── tests │ ├── test_datasets.py │ ├── test_evaluation.py │ ├── test_hmm.py │ └── 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