{"id":23236,"library":"alifedata-phyloinformatics-convert","title":"alifedata-phyloinformatics-convert","description":"A library for converting standardized ALife (artificial life) phylogenetic data formats (e.g., from hstrat, phylotrackpy) into formats compatible with traditional phyloinformatics software (e.g., Newick, Nexus, FASTA). Current version 0.19.3, requires Python >=3.8. Active development with monthly releases.","status":"active","version":"0.19.3","language":"python","source_language":"en","source_url":"https://github.com/mmore500/alifedata-phyloinformatics-convert","tags":["phylogenetics","alife","conversion","bioinformatics"],"install":[{"cmd":"pip install alifedata-phyloinformatics-convert","lang":"bash","label":"Default install"}],"dependencies":[],"imports":[{"note":"AlifeDataConvert is the main class for conversion. Wrong imports (e.g., AlifeDataConvert spelled differently) cause ImportError.","wrong":"from alifedata_phyloinformatics_convert import SomethingElse","symbol":"AlifeDataConvert","correct":"from alifedata_phyloinformatics_convert import AlifeDataConvert"},{"note":"Common mistake: forgetting to use the alias adpc or misspelling the module name (underscores vs hyphens).","wrong":"import alifedata_phyloinformatics_convert","symbol":"AlifeDataConvert","correct":"import alifedata_phyloinformatics_convert as adpc"}],"quickstart":{"code":"from alifedata_phyloinformatics_convert import AlifeDataConvert\n\n# Example: convert a simple Newick string to Nexus\nnewick_str = \"(A:0.1,B:0.2):0.3;\"\nconverter = AlifeDataConvert()\nnexus = converter.convert(newick_str, source_format='newick', target_format='nexus')\nprint(nexus)","lang":"python","description":"Initialize the converter and convert between formats. The source and target formats can be 'newick', 'nexus', 'fasta', etc."},"warnings":[{"fix":"Install: pip install alifedata-phyloinformatics-convert\nImport: import alifedata_phyloinformatics_convert","message":"The package name uses hyphens, but Python import requires underscores. Use pip install with hyphens, but import with underscores.","severity":"gotcha","affected_versions":"all"},{"fix":"Always provide both source_format and target_format explicitly in the call to convert().","message":"Version 0.19.0 changed the signature of AlifeDataConvert.convert() – the 'source_format' and 'target_format' parameters are now required (previously optional). Code that relied on defaults will break.","severity":"breaking","affected_versions":">=0.19.0"},{"fix":"Consult the official GitHub README for supported conversion matrix. Currently supports: newick, nexus, fasta, phylip (some combinations).","message":"The library only supports specific format pairs (e.g., newick->nexus, newick->fasta). Check the documentation for the exact list of supported conversions before use.","severity":"gotcha","affected_versions":"all"}],"env_vars":null,"last_verified":"2026-05-01T00:00:00.000Z","next_check":"2026-07-30T00:00:00.000Z","problems":[{"fix":"pip install alifedata-phyloinformatics-convert\nThen in Python: import alifedata_phyloinformatics_convert","cause":"The package was installed with hyphens in the name but Python import expects underscores.","error":"ModuleNotFoundError: No module named 'alifedata_phyloinformatics_convert'"},{"fix":"Update call to include both arguments, e.g., converter.convert(newick_str, source_format='newick', target_format='nexus')","cause":"Code written for older version where these arguments were optional; now required as of 0.19.0.","error":"TypeError: convert() missing 2 required positional arguments: 'source_format' and 'target_format'"}],"ecosystem":"pypi","meta_description":null,"install_score":null,"install_tag":null,"quickstart_score":null,"quickstart_tag":null}