├── .gitignore ├── CHANGELOG.md ├── LICENSE.md ├── Makefile ├── README.md ├── bioconda_test.sh ├── dev ├── Makefile-crossplat-dev ├── TODO.md └── phyloacc-cfg-dev.yaml ├── docs └── v1 │ ├── READMEv1.md │ ├── READMEv1_OUTPUT.md │ └── READMEv1_PARAMETER.md ├── phyloacc-cfg-template.yaml └── src ├── PhyloAcc-GT ├── Makefile ├── bpp.cpp ├── bpp.hpp ├── bpp_c.cpp ├── bpp_c.hpp ├── bpp_c2.cpp ├── genetree.cpp ├── genetree.hpp ├── main.cpp ├── newick.cpp ├── newick.h ├── newick2.cpp ├── newick2.h ├── placeholder ├── profile.cpp ├── profile.h ├── utils.cpp └── utils.h ├── PhyloAcc-ST-GBGC ├── Makefile ├── PhyloAcc_gBGC └── SRC │ ├── bpp.cpp │ ├── bpp.hpp │ ├── bpp_c.cpp │ ├── bpp_c.hpp │ ├── bpp_c2.cpp │ ├── main.cpp │ ├── newick.cpp │ ├── newick.h │ ├── profile.cpp │ ├── profile.h │ ├── utils.cpp │ └── utils.h ├── PhyloAcc-ST ├── Makefile ├── bpp.cpp ├── bpp.hpp ├── bpp_c.cpp ├── bpp_c.hpp ├── bpp_c2.cpp ├── main.cpp ├── newick.cpp ├── newick.h ├── profile.cpp ├── profile.h ├── utils.cpp └── utils.h └── PhyloAcc-interface ├── phyloacc.py ├── phyloacc_lib ├── __init__.py ├── batch.py ├── cf.py ├── core.py ├── html.py ├── info.yaml ├── labeltree.py ├── opt_parse.py ├── output.py ├── pa-welcome.txt ├── params.py ├── plot.py ├── post_opt_parse.py ├── post_params.py ├── seq.py ├── templates.py ├── templates_post.py ├── tree.py ├── tree_old.py └── treeio.py └── phyloacc_post.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/phyloacc/PhyloAcc/HEAD/.gitignore -------------------------------------------------------------------------------- /CHANGELOG.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/phyloacc/PhyloAcc/HEAD/CHANGELOG.md -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- 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