{"id":19107933,"url":"https://github.com/haschka/mnhn-tree-tools","last_synced_at":"2026-03-19T08:08:34.635Z","repository":{"id":90645083,"uuid":"325312749","full_name":"haschka/mnhn-tree-tools","owner":"haschka","description":"MNHN-Tree-Tools a software for phylogenetic inference of millions of sequences","archived":false,"fork":false,"pushed_at":"2026-01-02T10:42:56.000Z","size":21464,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"master","last_synced_at":"2026-01-08T11:26:16.069Z","etag":null,"topics":["bioinformatics","bioinformatics-tool","dbscan","phylogenetics","tree-of-life","tree-structure","unix-tools"],"latest_commit_sha":null,"homepage":"http://treetools.haschka.net","language":"Roff","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/haschka.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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2020-12-29T14:50:36.000Z","updated_at":"2026-01-02T10:43:01.000Z","dependencies_parsed_at":"2025-08-13T12:21:44.793Z","dependency_job_id":null,"html_url":"https://github.com/haschka/mnhn-tree-tools","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/haschka/mnhn-tree-tools","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haschka%2Fmnhn-tree-tools","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haschka%2Fmnhn-tree-tools/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haschka%2Fmnhn-tree-tools/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haschka%2Fmnhn-tree-tools/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/haschka","download_url":"https://codeload.github.com/haschka/mnhn-tree-tools/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haschka%2Fmnhn-tree-tools/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29976272,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-01T16:35:47.903Z","status":"ssl_error","status_checked_at":"2026-03-01T16:35:44.899Z","response_time":124,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":["bioinformatics","bioinformatics-tool","dbscan","phylogenetics","tree-of-life","tree-structure","unix-tools"],"created_at":"2024-11-09T04:14:26.853Z","updated_at":"2026-03-01T17:01:54.999Z","avatar_url":"https://github.com/haschka.png","language":"Roff","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Manual\n\n* Please note that there is full manual with detailed build and usage \n  instruction as well as a tutorial available at\n  https://github.com/haschka/mnhn-tree-tools-manual/blob/master/manual.pdf\n\n# How to build (Debain 10 / Ubuntu 20.04  with standard non optimzed libraries)\n```\nsudo apt-get install git build-essential libpng-dev libsdl2-dev liblapack-dev libopenmpi-dev libpocl-dev ocl-icd-opencl-dev pocl-opencl-icd\n\ngit clone https://github.com/haschka/mnhn-tree-tools\n\ncd mnhn-tree-tools\nmkdir bin\nmake all\ncd bin\n\n# make MNHN-TREE-TOOLS available from any folder ( this is temporary, you\n# may modify your .bashrc and similar files to make this permanent\nexport PATH=$PATH:$PWD\n```\n\n# How to build (generic and optimized)\n\n* create a bin subdirectory: i.e. by typing `mkdir bin`\n\n* install libSDL2, libpng, mpi and OpenCL on your distribution/unix-system\ntogether with the development version of packages (i.e. with header files)\n\nMPI has been tested to work with OpenMPI but may work with other version.\n\nOpenCL has been tested with the version shipped with the Nvidia Cuda Toolkit \nand the Intel OpenCL SDK. The later is only available for code generation on \nCPUs and hence only interesting for debugging purposes where a GPU is \nnot available.\n\n* edit the makefile, i.e. `emacs makefile`\nadjust the header of the makefile to point to the correct locations \nof the libraries on your distribitution.\n\n* type `make all`\n\nif everything goes well you should have all the tools available in the bin\nfolder.\n\n* Flaws\n\nCurrently only works on 64 bit machines where size_t and pointers are 64bits\nlong.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhaschka%2Fmnhn-tree-tools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhaschka%2Fmnhn-tree-tools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhaschka%2Fmnhn-tree-tools/lists"}