{"id":16282375,"url":"https://github.com/zsailer/pyasr","last_synced_at":"2025-09-13T21:48:05.263Z","repository":{"id":62578745,"uuid":"108433791","full_name":"Zsailer/pyasr","owner":"Zsailer","description":"Ancestral Sequence Reconstruction in Python","archived":false,"fork":false,"pushed_at":"2019-05-09T15:30:20.000Z","size":694,"stargazers_count":13,"open_issues_count":2,"forks_count":8,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-03-04T18:02:41.811Z","etag":null,"topics":["evolution","pandas","phylogenetics","python"],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Zsailer.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}},"created_at":"2017-10-26T15:59:03.000Z","updated_at":"2025-01-13T07:45:50.000Z","dependencies_parsed_at":"2022-11-03T21:00:44.880Z","dependency_job_id":null,"html_url":"https://github.com/Zsailer/pyasr","commit_stats":null,"previous_names":[],"tags_count":10,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Zsailer%2Fpyasr","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Zsailer%2Fpyasr/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Zsailer%2Fpyasr/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Zsailer%2Fpyasr/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Zsailer","download_url":"https://codeload.github.com/Zsailer/pyasr/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244538518,"owners_count":20468728,"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":["evolution","pandas","phylogenetics","python"],"created_at":"2024-10-10T19:10:29.359Z","updated_at":"2025-03-20T02:30:30.005Z","avatar_url":"https://github.com/Zsailer.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# PyASR\n\n**Ancestral Sequence Reconstruction in Python**\n\nPyASR offers a modern Python interface to [PAML](http://abacus.gene.ucl.ac.uk/software/paml.html) (\"Phylogenetic Analysis by Maximum Likelihood\")--tuned specifically for reconstruction\nancestral protein/DNA sequences.\n\n**NOTE:** PyASR currently only supports protein reconstructions. This is a work in progress.\n\n## Basic Usage\n\n```python\nimport phylopandas as pd\nimport dendropy as d\nimport pyasr\n\n# Use phylopandas to read a set of ancestor.s\ndf_seqs = pd.read_fasta('test.fasta')\n\n# Use dendropy to read in tree.\ntree = d.Tree.get(path='tree.newick', schema='newick')\n\n# Reconstruct nodes in tree.\ntree, df_seqs, df_anc = pyasr.reconstruct(df_seqs, tree, working_dir='test', alpha=1.235)\n\n# Write out ancestor dataframe to a CSV file.\ndf_anc.to_csv('ancestors.csv')\n```\n\nWe can visualize the ancestors side-by-side with the tree using inside of JupyterLab\nthanks to the ToyTree library.\n\n\u003cimg src=\"docs/jlab-example.png\" align=\"middle\"\u003e\n\n## Install\n\nThis package is released on PyPi. You can install using pip:\n```\npip install pyasr\n```\n\nTo get the development version:\n```\ngit clone\ncd\npip install -e .\n```\n\n## Dependencies\n\nThe actual reconstruction calculation are done using [PAML](http://abacus.gene.ucl.ac.uk/software/paml.html). This requires PAML to be\ninstalled and the `codeml`/`baseml` executables exported to your `$PATH` environment variable. Directions for installing PAML can be found on the PAML website.\n\nThe following Python dependencies are required for PyASR to work.\n\n- Pandas\n- Biopython\n- PhyloPandas\n- DendroPy\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzsailer%2Fpyasr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fzsailer%2Fpyasr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzsailer%2Fpyasr/lists"}