{"id":17595200,"url":"https://github.com/dcasella/persistent-phylogeny","last_synced_at":"2025-03-29T19:41:53.843Z","repository":{"id":74791490,"uuid":"106341616","full_name":"dcasella/persistent-phylogeny","owner":"dcasella","description":"An implementation for the persistent phylogeny polynomial-time algorithm","archived":false,"fork":false,"pushed_at":"2018-05-12T18:01:53.000Z","size":268,"stargazers_count":3,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-03-26T02:51:25.715Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/dcasella.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-10-09T22:26:07.000Z","updated_at":"2019-11-28T12:17:12.000Z","dependencies_parsed_at":null,"dependency_job_id":"cbd96ba2-4ed5-4a05-a892-88cd4f71a4aa","html_url":"https://github.com/dcasella/persistent-phylogeny","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dcasella%2Fpersistent-phylogeny","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dcasella%2Fpersistent-phylogeny/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dcasella%2Fpersistent-phylogeny/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dcasella%2Fpersistent-phylogeny/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dcasella","download_url":"https://codeload.github.com/dcasella/persistent-phylogeny/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246237414,"owners_count":20745346,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-10-22T07:43:52.837Z","updated_at":"2025-03-29T19:41:53.809Z","avatar_url":"https://github.com/dcasella.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Persistent Phylogeny\n\nAn implementation for the persistent phylogeny polynomial-time algorithm described the article [Solving the Persistent Phylogeny Problem in polynomial time](https://arxiv.org/abs/1611.01017).\n\n## Prerequisites\n\n- gcc 5.0 and above\n- [Boost libraries](http://www.boost.org/more/getting_started/index.html)\n\n## Compiling\n\n### Get Boost\n\n\u003e N.B. Skip this block if you already have Boost on your system\n\n#### From repository\n\nPopular Linux and Unix distributions such as Fedora, Debian, and NetBSD include pre-built Boost packages.\n\nDebian example:\n\n```\n# apt install libboost-all-dev\n```\n\n#### From source\n\nDownload Boost.\n\n- Unix: follow the steps at [boost.org](http://www.boost.org/doc/libs/1_65_1/more/getting_started/unix-variants.html)\n- Windows: follow the steps at [boost.org](http://www.boost.org/doc/libs/1_65_1/more/getting_started/windows.html)\n\n##### Boost.ProgramOptions\n\n\u003e N.B. Skip this step if you already built Boost on your system\n\nThis implementation uses `Boost.ProgramOptions` to parse command line arguments and options, which means it needs separately-compiled library binaries to work.\n\n- Unix: follow the steps at [boost.org](http://www.boost.org/doc/libs/1_65_1/more/getting_started/unix-variants.html#prepare-to-use-a-boost-library-binary)\n- Windows: follow the steps at [boost.org](http://www.boost.org/doc/libs/1_65_1/more/getting_started/windows.html#prepare-to-use-a-boost-library-binary)\n\n\u003e NB. Skip this step if you already updated your platform's environment variable\n\nMoreover, on Unix systems, you may need to prepare plaform-specific settings (since `Boost.ProgramOptions` is a shared library).\n\n- Follow the steps at [boost.org](http://www.boost.org/doc/libs/1_65_1/more/getting_started/unix-variants.html#test-your-program)\n\n### Clone the repository\n\n```\n$ git clone https://github.com/dcasella/persistent-phylogeny.git\n$ cd persistent-phylogeny\n```\n\n### Compile and link\n\n```\n$ make\n```\n\n## Usage\n\n```\nppp [OPTION...] FILE...\n```\n\n**ppp** corresponds to the executable binary.\n\n**OPTION** is a list of options - can be omitted.\n\n**FILE** is a list of file paths (1 or more).\n\n### Options\n\n```\n-h or  --help\n```\n\nDisplay this message.\n\n___\n\n```\n-v or --verbose\n```\n\nDisplay the operations performed by the program.\n\n___\n\n```\n-t or --testpy\n```\n\nTest the output of the algorithm with check_reduction.py.\nThis can be used to make sure the output of the program is correct.\n**Don't** use this option when benchmarking; the Python script takes time to complete.\n\n___\n\n```\n-x or --exponential\n```\n\nExponential version of the algorithm.  \nThis option can be used to test every possible combination of safe sources.  \nIt is also mutually exclusive with `--interactive` and `--nthsource`.\n\n___\n\n```\n-i or --interactive\n```\n\nUser input driven execution.  \nThis option can be used to manually select which safe source to realize.  \nIt is also mutually exclusive with `--exponential` and `--nthsource`.\n\n___\n\n```\n-m or --maximal\n```\n\nRun the algorithm on the maximal subgraph instead of the full graph.  \nThis is done by calculating a maximal reducible graph before running the algorithm.\n\n___\n\n```\n-n N or --nthsource N\n```\n\nSelect the nth safe source when possible (default 0 - the option can be omitted).  \nThis option can be used to automatically select the nth safe source to realize (instead of manually selecting it each time with `--interactive`).  \nIt is also mutually exclusive with `--exponential` and `--interactive`.\n\n## Running\n\n```\n$ ./bin/ppp FILE...\n```\n\nThe program will call the `reduce` function on each graph read from the files.\n\nExamples:\n\nListing the single files\n\n```\n$ ./bin/ppp file1 dir1/file2 dir1/file3\n```\n\nOr with globs (if your shell supports it)\n\n```\n$ ./bin/ppp dir1/*\n```\n\nOr with options (order doesn't matter - still supports globs)\n\n```\n$ ./bin/ppp -m -v file1\n```\n\n## Input file structure\n\nThe first line must contain the size of the matrix.  \nEmpty lines (after the first) are ignored.  \nSubsequent lines represent the matrix itself.\n\n```\nN M\n\nMatrix made up of space-separated boolean values\n```\n\nExample:\n\n```\n6 3\n\n0 0 1\n0 1 0\n0 1 1\n1 0 0\n1 0 1\n1 1 0\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdcasella%2Fpersistent-phylogeny","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdcasella%2Fpersistent-phylogeny","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdcasella%2Fpersistent-phylogeny/lists"}