Brandon Invergo

seqmi

Gitlab page

seqmi

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.

Installation

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 particular, the --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 tests.

Usage

For a quick overview of all of the options available, run seqmi with the --help (-?) 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 running make pdf or make html, respectively.