├── .gitattributes ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── divsufsort ├── config.h ├── divsufsort.c ├── divsufsort.h ├── divsufsort64.h ├── divsufsort_private.h ├── sssort.c ├── trsort.c └── utils.c ├── ez_setup.py ├── probcons ├── CompareToRef.cc ├── Defaults.h ├── EvolutionaryTree.h ├── FileBuffer.h ├── FixRef.cc ├── MakeGnuPlot.cc ├── MultiSequence.h ├── ProbabilisticModel.h ├── Probcons.cc ├── ProjectPairwise.cc ├── SafeVector.h ├── ScoreType.h ├── Sequence.h └── SparseMatrix.h ├── reveal ├── __init__.py ├── align.py ├── annotate.py ├── bubbles.py ├── chain.py ├── chop.py ├── comp.py ├── convert.py ├── extract.py ├── matches.py ├── merge.py ├── plot.py ├── refine.py ├── rem.py ├── reveal.py ├── schemes.py ├── split.py ├── stats.py ├── subgraph.py ├── tests │ ├── __init__.py │ └── test_reveal.py ├── transform.py ├── transformold.py ├── unzip.py └── utils.py ├── reveallib ├── interface.c ├── reveal.c └── reveal.h ├── setup.py ├── tests ├── 123a.fa ├── 123b.fa ├── 1a.fa ├── 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