├── IMfig ├── IMa3_3pop_example.out ├── IMfig.py └── Using_the_IMfig_program.pdf ├── LICENSE ├── Makefile ├── README ├── alltreestrings.cpp ├── autoc.cpp ├── burnphylogenycounts.cpp ├── calc_prob_data.cpp ├── chainprint.cpp ├── documentation ├── IMa2_IMa3_commandline_conversion_cheatsheat.txt └── Using_IMa3.pdf ├── freemem.cpp ├── gewekeIM.cpp ├── ginfo.cpp ├── gtint.cpp ├── histograms.cpp ├── ima.hpp ├── ima_main.cpp ├── initialize.cpp ├── jointfind.cpp ├── marglike.cpp ├── mcmcfile.cpp ├── msdirent.cpp ├── msdirent.hpp ├── multi_t_bins.cpp ├── output.cpp ├── popmig.cpp ├── readata.cpp ├── readpriorfile.cpp ├── surface_call_functions.cpp ├── surface_search_functions.cpp ├── swapchains.cpp ├── testbed ├── README.txt ├── ima3_priorfile_3pops.txt ├── ima3_stdtest.sh ├── ima3_stdtest1.bat ├── ima3_stdtest2.bat ├── ima3_stdtest_notes.txt ├── ima3test3pop4loci.u ├── ima3test4pop2loci.u ├── ima3test4pop5loci.u ├── ima3test8pop2loci.u ├── pop3_nested_model_test.txt └── randNums ├── tinystr.cpp ├── tinystr.hpp ├── tinyxml.cpp ├── tinyxml.hpp ├── tinyxmlerror.cpp ├── tinyxmlparser.cpp ├── treeprint.cpp ├── update_gtree.cpp ├── update_gtree.hpp ├── update_gtree_common.cpp ├── update_gtree_common.hpp ├── update_hg.cpp ├── update_mc_params.cpp ├── update_poptree.cpp ├── update_priors.cpp ├── update_t_NW.cpp ├── update_t_RY.cpp ├── update_t_RYhg.cpp ├── utilities.cpp └── windows_exec_and_doc.zip /IMfig/IMa3_3pop_example.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jodyhey/IMa3/HEAD/IMfig/IMa3_3pop_example.out -------------------------------------------------------------------------------- /IMfig/IMfig.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jodyhey/IMa3/HEAD/IMfig/IMfig.py -------------------------------------------------------------------------------- /IMfig/Using_the_IMfig_program.pdf: 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