Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignments provide a basis for research into comparative genomics and the study of genome-wide evolutionary dynamics.
Mauve has been developed with the idea that a multiple genome aligner should require only modest computational resources. It employs algorithmic techniques that scale well in the lengths of sequences being aligned. For example, a pair of Y. pestis genomes can be aligned in under a minute, while a group of 9 divergent Enterobacterial genomes can be aligned in a few hours. However, the current algorithm’s compute time (progressiveMauve) scales cubically in the number of genomes to align, making it unsuitable for datasets containing more than 50-100 bacterial genomes.
Mauve development began at the University of Wisconsin-Madison with a team including Aaron Darling, Bob Mau, and Nicole Perna. Several others have contributed development to aspects of the Mauve software in the time since. Unfortunately, the software seems to be unmaintained at this time.
This version has a patched mauve-gui which allows it to run on modern systems.
The orignal unpatched Mauve build instructions are included in the file BUILD_INSTRUCTIONS.txt. On Ubuntu 19.04 it is possible to install Mauve using:
sudo apt-get install mauve
To use Mauve, first download this repository, change to its directory, and compile with:
ant compile # compiles all the java files into class files
ant jar # creates Mauve.jar
and then you can run Mauve with:
java -jar Mauve.jar
You may want to use a different maximum heap size with the appropriate -Xmx option, for example java -Xmx10G -jar Mauve.jar for a 10 GB memory size. Depending on what you do, Mauve may need different values to operate correctly.
NOTE: for people with a high resolution display it is possible to scale the program by changing:
JAVA_ARGS="-Xms200M -Xmx10G -Dsun.java2d.uiScale=2.5"