There are several software packages and modules developed in Python. If some provided extended facilities and full-featured Graphical User Interfaces, others work on the language environment extending python native methods and attributes. Below you find a small list of such packages.
- Biopython - A set of freely available tools for biological computation
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and bioinformatics.
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Pycogent - Comparative Genomic Toolkit. Another popular and extensive library for genomic biology.
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PyChem - A cross-platform open source package for multivariate analysis, that includes a graphical user interface.
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bx-python - Library and associated set of scripts to allow for rapid implementation of genome scale-analyses.
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p4 - Python package for phylogenetics, useful for programmatic manipulation of phylogenetic data and trees, including maximum likelihood and Bayesian inference.
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p3d - Python module for structural bioinformatics. p3d is the perfect tool to quickly develop structural bioinformatical tools that can perform rapid and complex analyses of protein structures using the Python scripting language.
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UCSF Chimera - UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials, and can be downloaded free of charge for academic, government, non-profit, and personal use.
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Modeller - used for homology or comparative modeling of protein three-dimensional structures. Control scripts are Python based.
- PyMol - 3D molecular viewer, suitable (and widely used) for publications and presentations. Fully scriptable in Python.