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# Mimosa - Miniature Model Organism Sequence Aligner

## What is Mimosa?

Mimosa is a application which provides an web interface to various sequence
alignment programs and sequence databases. Currently BLAST is supported, and
support for other alignment programs, such as BLASTP and BWA are planned.

## What does Mimosa do?

Mimosa allows evolutionary researchers to run sequence alignment programs on
nucleotides or proteins, and request sequences from various sequence databases,
all from a friendly web interface.

## Who is Mimosa for?

Mimosa is intended to be used by evolutionary biology researchers who do
sequence alignment against sets of nucleotide or protein data. These sets could
all be for different organisms, or all the same organism. Mimosa doesn't care.

If the data is public, Mimosa can be installed on a publicly-availabe website,
and allow sequence aligment by collaborators. If the data is pre-publication
and still actively changing, Mimosa can also be setup to only be accessed by
certain persons, either people on the local intranet, or those logging in with
a username and password.

## Why does Mimosa exist? Aren't there a lot of things that already do this?

Mimosa exists to solve the problem of making a standalone sequence alignment
web interface. All existing sequence alignment web interfaces are either tightly
coupled to legacy codebases, difficult to deploy, or just plain *unfriendly* to
end users.

Mimosa plans on being an easy-to-install standalone sequence aligner, which
can be integrated into an existing website via a REST interface.

## How do I get Mimosa?

You can install Mimosa from CPAN (where it is called
[http://p3rl.org/App::Mimosa](App::Mimosa)) .

If you use cpanminus (preferred) :

    cpanm App::Mimosa

If you use CPAN.pm:

    cpan App::Mimosa

### Installing non-Perl dependencies

Mimosa requires the 'fastacmd' binary and some image libraries. If you are on
a Debian-ish system, you can install these with apt-get:

    apt-get install libgd2-xpm-dev blast2

### Cloning via Git

If you have cpanminus:

    git clone git://github.com/GMOD/mimosa.git
    cd mimosa
    cpanm --installdeps . # install necessary Perl dependencies
    perl Build.PL
    ./Build

If you don't have cpanminus:

    git clone git://github.com/GMOD/mimosa.git
    cd mimosa
    perl Build.PL
    ./Build --installdeps # install necessary Perl dependencies
    ./Build

## How do I run the Mimosa test suite ?

After you have run the command

    perl Build.PL

you can either type:

    ./Build test

or use prove: