A continuation of exonerate, a generic tool for sequence alignment by Guy St. C. Slater et al. (http://www.ebi.ac.uk/~guy/exonerate/).
Exonerate is apparently unmaintained. The goal of this fork is mainly bug fixes to the final version (2.4.0).
To check out/build the final (stable) version:
$ git clone https://github.com/nathanweeks/exonerate.git
$ cd exonerate
$ git checkout v2.4.0
$ ./configure [YOUR_CONFIGURE_OPTIONS]
$ make
$ make check
$ make install
To build the development version (at your own risk!):
$ git clone https://github.com/nathanweeks/exonerate.git
$ cd exonerate
$ git checkout develop
$ autoreconf -i
$ ./configure [YOUR_CONFIGURE_OPTIONS]
$ make
$ make check
$ make install