├── .gitignore ├── .travis.yml ├── LICENSE ├── README.md ├── src ├── bank │ ├── MLST.h │ ├── approxdf.h │ ├── census.h │ ├── cmatrix.h │ ├── coalesce.h │ ├── coalescent_control.h │ ├── coalescent_process.h │ ├── controlwizard.h │ ├── ess.h │ ├── mutation.h │ ├── pause.h │ ├── readme.doc │ ├── revolver.h │ ├── sort.h │ └── tsv.h ├── brent.h ├── cfml_results.R ├── coalesce │ └── coalescent_record.h ├── main.cpp ├── main.h ├── make.sh ├── makefile ├── myutils │ ├── DNA.h │ ├── argumentwizard.h │ ├── lotri_matrix.h │ ├── matrix.h │ ├── mydouble.h │ ├── myerror.h │ ├── myutils.h │ ├── newick.h │ ├── random.h │ ├── utils.h │ └── vector.h ├── powell.h └── xmfa.h └── testdata ├── test.fasta └── test.nwk /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/xavierdidelot/ClonalFrameML/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: 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