comparem 0.0.10

A toolbox for comparative genomics.

# CompareM

<b>[This project is in active development, you are welcomed to use this software though it may be unstable.]</b>

CompareM is a comparative genomics toolbox. It provides statistics across groups of genomes (e.g., amino acid identity; core, dispensible, and unique gene sets) and for individual genomes (e.g., GC content, coding density, codon usage). Emphasis has been placed on providing parallelized implementations in order to allow scalability to thousands of genomes. The functionality currently planned is:

<i>Comparative genomic statistics:</i> * average amino acid identity (AAI) between genomes * average nucleotide identity (ANI) between genomes * core, dispensible, and unique gene sets

<i>Single genome statistics:</i> * GC content * coding density * codon and amino acid usage * automatic identification of translation table * N50; maximum and mean scaffold/contig size; no. of scaffolds/contigs

<i>Genomic usage patterns:</i> * codon usage * amino acid usage * kmer usage for k <= 8 (e.g., tetranucleotide) * stop codon usage * Visualization of usage patterns with PCA plots and hierarchical clustering dendrograms

A number of auxillary tools are also provides which are often helpful within comparative genomic studies: * identification of homologous genes followed by alignment and tree inference * back-translation of amino acid alignments to nucleotides

## Install

The simplest way to install this package is through pip: > sudo pip install comparem

This package requires the numpy and biolib python packages to be installed, and makes use of the follow bioinformatic programs:

• [prodigal](http://prodigal.ornl.gov/) >= 2.6.2: Hyatt D, Locascio PF, Hauser LJ, Uberbacher EC. 2012. Gene and translation initiation site prediction in metagenomic sequences. <i>Bioinformatics</i> 28: 2223-2230.

• [blast+](http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download) >= 2.2.30+: Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. 2009. BLAST+: architecture and applications. <i>BMC Bioinformatics</i> 10:421: doi: 10.1186/1471-2105-10-421.

• [diamond](http://ab.inf.uni-tuebingen.de/software/diamond/) >= 0.7.12: Buchfink B, Xie C, Huson DH. 2015. Fast and sensitive protein alignment using DIAMOND. <i>Nature Methods</i> 12: 59–60 doi:10.1038/nmeth.3176.

## Cite

If you find this package useful, please cite this git repository (https://github.com/dparks1134/CompareM)

## Copyright

Copyright © 2014 Donovan Parks. See LICENSE for further details.