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        "author": "Matt Gibson, Mark Hibbins",
        "author_email": "matthewjsgibson@gmail.com, mhibbins@iu.edu",
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        "description": "# HemiplasyTool\n\n\n![](https://img.shields.io/github/release-pre/mhibbins/hemiplasytool.svg)\n![](https://img.shields.io/github/release-date-pre/mhibbins/hemiplasytool.svg)\n## Authors:\nMatt Gibson (gibsomat@indiana.edu)  \nMark Hibbins (mhibbins@indiana.edu)\n\n## Dependencies:\n* [ms](http://home.uchicago.edu/~rhudson1/source.html)  \n* [seq-gen](http://tree.bio.ed.ac.uk/software/seqgen/)\n* biopython\n* numpy\n* matplotlib\n\n\n## Installation\n\n```\ngit clone https://github.com/mhibbins/hemiplasytool\ncd hemiplasytool\npython setup.py install\n```\n\n\n## Usage\n```\nusage: hemiplasytool [-h] [-v] [-n] [-x] [-p] [-g] [-s] [-o] splits\n\nTool for characterising hemiplasy given traits mapped onto a species tree\n\npositional arguments:\n  splits                Input file describing split times, trait pattern, and\n                        topology\n\noptional arguments:\n  -h, --help            show this help message and exit\n  -v, --verbose         Enable debugging messages to be displayed\n  -n , --replicates     Number of replicates per batch\n  -x , --batches        Number of batches\n  -p , --mspath         Path to ms\n  -g , --seqgenpath     Path to seq-gen\n  -s , --mutationrate   Seq-gen mutation rate (default 0.05)\n  -o , --outputdir      Output directory\n```\n\n## Input file\n\nThe input file has three sections:  split times, traits, and species tree. They must be specified in this order and delimited by a '#'. See below for descriptions of each section\n\n```\n#splits\n6   2   1\n3   3   2\n1.5 5   3\n1.25    6   5\n1   4   3\n\n#traits\n1   0 \n2   1\n3   0\n4   1\n5   0\n6   1\n\n#tree\n(1,(2,((6,5),(4,3))));\n\n#introgression (time, source, dest, probability; optional)\n0.25    3   2   0.1\n0.5 5   6   0.1\n\n```\n\n### Split times\n\nThe split times describe the order of subpopulation splits to `ms`. Each line specifies the timing (in 4N generations), source population, and destination population (backwards in time). Splits should be ordered oldest to newest. Entries should be delimited by spaces or tabs\n\n\n### Traits\n\nThe traits section describes the observed species trait pattern. Each line specifies the taxa ID (must correspond to those coded in the split times file), the binary trait value, and the timing of sampling (in 4N generations relative to the longest branch). These can be specified in any order\n\n\n### Species tree\n\nThe species tree in Newick format. Again, taxa IDs must correspond to those in the split times and traits sections.\n\n### Introgression\n\nIntrogression events. Each line should specify the timing (in 4N generations), source taxon, destination taxon, and probability of introgression. Events can be specified in any order.\n\n## Example:\n```\nhemiplasytool -v -n 1000000 -p ~/bin/ms -g ~/bin/seq-gen -x 1 ./input_test.txt\n```\n\n### Output:\n```\nOf the replicates that follow species site pattern:\n118 were discordant\n32 were concordant\n\n\nOn concordant trees:\n# Mutations\t# Trees\n3\t\t28\n4\t\t3\n5\t\t1\n\nOn discordant trees:\n# Mutations\t# Trees\n1\t\t5\n2\t\t21\n3\t\t70\n4\t\t20\n5\t\t2\n\nDerived mutation inheritance patterns for trees with fewer mutations than derived taxa:\n\n\tTerm\tInherited from anc node\nTaxa 2\t15\t6\nTaxa 4\t0\t21\nTaxa 6\t1\t20\n\nDEBUG:root:Plotting...\n\nTime elapsed: 47.09378099441528 seconds\n```\n\n![Mutation distribution](mutation_dist.png)\n\n",
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        "keywords": "phylogenetics evolution hemiplasy homoplasy",
        "license": "MIT",
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