mauve-py

Python wrappers for a fork of progressiveMauve multiple genome aligner

mauve-py is particularly suited to mapping modified synthetic genomes back to a reference genome and includes features to aid in the "healing" of the mapping that the progressive mauve binaries miss

See mauve alignment for original source. The Mauve License is GPLv2.

Please cite progressive mauve:

Aaron E. Darling, Bob Mau, and Nicole T. Perna. 2010.  
progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss, 
and Rearrangement.  PLoS One.  5(6):e11147. 

All dependencies are grouped in this repo which include MUSCLE. MUSCLE is licensed in the Public Domain

For MUSCLE cite:

Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy 
and high throughput Nucleic Acids Res. 32(5):1792-1797

The included Python wrappers and file parsers are GPLv2 Licensed Copyright (c) 2014 Nick Conway, Ben Pruitt; Wyss Institute for Biologically Inspired Engineering

Usage

Right now we support comparing only two genomes at a time, although mauve will handle more.

Use fasta files on the input:

import mauve
index_lookup_table = mauve.buildIndex("my_genome_A.fa", "reference_genome_B.fa")

the index_lut is a lookup table mapping a modified genome A index to a reference genome B index from the 5' end starting at 0.

Dependencies

Binary dependencies

Get these for your platform (Linux or OS X, Windows is unsupported)

• automake
• libtool
• pkg-config
• boost > 1.55

Which can easily be installed with the package manager for your OS, apt, yum, etc on Linux, or Homebrew for OS X

Python dependencies

• numpy
• bitarray
• cython
• libnano

which can all be installed with pip except libnano

LINUX INSTALLATION (Debian)

Double check you have the right boost components installed

boost requirements for debian linux

libboost-filesystem-dev, libboost-program-options-dev, libboost-iostreams-dev

run:

python setup.py install

OS X INSTALLATION (Mavericks tested)

Double check you have the right boost components installed

make sure you have Homebrew installed on OS X Mavericks

brew install boost --c++11

run:

python setup.py install

see:

• clang boost ref 1
• clang boost ref 2

Building Mauve stand-alone

If you'd like to use mauve without the python wrapper, look in the mauve/src path for the fork of the source. It is updated to build on recent gcc and clang with c++11, mainly out of the need to get rid of build errors and warnings.

Deviations from stock mauve

• updated to latest boost 1.55ish so we now run BOOST_FILESYSTEM_VERSION 3 instead of 2
• OS X is clang compatible now. follow instructions below.
• no Windows support although it might be easy to add back in
• lots of compiler warning fixes thanks to building on both clang and gcc