seqmi is a tool for calculating mutual information (MI) between amino acid residues in multiple sequence alignments. In addition to computing standard MI, it also supports calculating some MI corrections/adjustments.
If you are building this software directly from a clone of the
development repository, see the file
README-hacking for additional
instructions on building the software.
Otherwise, simply use the configure script and the Makefile to build and install seqmi:
$ ./configure $ make all $ make install
To see configuration options, run
./configure --help. In
--prefix option allows you to set the installation
location and the
--as-published option enables strict interpretation
of previously published methods (see RCW, below).
Unit tests are available via the
make check command. Note that
DejaGnu is required to run the
For a quick overview of all of the options available, run seqmi with
-?) option or view the provided man page.
At a minimum, you just need an alignment file. Currently, only FASTA format is supported. By default, this will calculate MI for all positions against all other positions.
$ seqmi alignment.fasta
For more options, see the included documentation. If you have texinfo
installed, just run
info seqmi. You can build PDF or HTML
documentation by changing to the
doc directory in this archive and
make pdf or
make html, respectively.