Welcome to pyani’s documentation!¶
Description¶
pyani is a program and Python package that provides support for calculating average nucleotide identity (ANI) and related measures for whole genome comparisons, and for rendering relevant graphical and tabular summary output. Where available, it natively takes advantage of multicore systems, and can integrate with SGE or OGE-compatible job schedulers to manage the computationally-heavy sequence comparisons.
Installing the pyani Python package also installs the program pyani, which enables command-line based analysis of genomes. Results are stored in a private SQLite3 database local to the machine, which permits addition of genomes to a previous analysis without having to recalculate all previously-performed comparisons, facilitating incremental analysis and visualisation, and enabling incremental maintenance of results for a taxonomic group as new genome sequences become available.
If you use pyani in your work, we would be grateful if you could please cite us as indicated on the Citations page.
Reporting problems and requesting improvements¶
If you encounter bugs or errors, or would like to suggest ways in which pyani can be improved, please raise a new issue at the pyani GitHub issues page.
If you’d like to fix a bug or make an improvement yourself, contributions are welcomed, and guidelines on how to do this can be found at the Contributing to pyani documentation page.
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