Python libraries and utilities for computational biology.
This package contains algorithms related to several areas of genomics, phylogenetics, and population genetics. Some of the highlights include:
- reading, writing, and manipulating phylogenetic trees
- reconciling gene-trees with species-trees
- inferring gene duplications, losses, and horizontal transfers
- methods for coalescent processes, incomplete lineage sorting
- methods for ancestral recombination graphs (ARGs)
- finding syntenic regions (i.e. co-linear orthology) between genomes
- processing common file formats: FASTA, PHYLIP, newick, nexus, etc.
In addition to computational biology-specific methods, this package also contains general utilities for working with scientific data:
- sparse matrix file formats
- reading, writing, and manipulating tables of data
- working with intervals (e.g. intersection, union, etc)
- plotting (Gnuplot, Rpy)
- statistics
- general data-structures and algorithms: quad trees, Union-Find, HHMs, clustering
The compbio package is available for download from several sources:
Most modules in this package can be used without any additional dependencies.
For plotting modules, the dependencies include:
For some scientific methods, the dependencies include:
For development of the compbio package itself, dependencies can be installed
with pip:
pip install -r requirements-dev.txt
The compbio package is available on pypi, and can be installed using pip:
pip install compbio
These packages can be installed from the source directory using:
python setup.py install
Optionally, the libraries can be used directly from the source directory by configuring one's environment variables as follows (assuming bash shell):
export PATH=$PATH:path/to/compbio/bin
export PYTHONPATH=$PYTHONPATH:path/to/compbio
These libraries were built up over the course of the Ph.D. of the author, Matthew D. Rasmussen (http://mattrasmus.com, [email protected]). Many of the methods here were utilized in several published software projects including:
- ARGweaver: Rasmussen, Siepel. Genome-wide inference of ancestral recombination graphs. ArXiv. 2013.
- DLCoal: Rasmussen, Kellis. Unified modeling of gene duplication, loss, and coalescence using a locus tree. Genome Research. 2012.
- SPIMAP: Rasmussen, Kellis. A Bayesian approach for fast and accurate gene tree reconstruction. Molecular Biology and Evolution. 2010.
- SPIDIR: Rasmussen, Kellis. Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes. Genome Research. 2007.
Minor note: Although the libraries of this package supports each of these software packages, this package is not a required dependency. Instead each software package contains its own private copy of modules taken from this package.