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<h1>glam2format Manual</h1>
<p>This program reads in a motif found by glam2, and writes it in a
standard alignment format (FASTA-with-gaps or MSF). This enables the
alignment to be passed to third-party software, including graphical
visualization tools such as <a
href="http://msa.cgb.ki.se/">Kalignvu</a>, <a
href="http://www.ch.embnet.org/software/BOX_form.html">Boxshade</a>,
and <a href="http://weblogo.berkeley.edu/">WebLogo</a>. On the other
hand, not all the motif information is preserved: in particular, the
key positions are lost. Only the top motif in glam2 output is
converted.</p>
<ul>
<li>Basic usage:
<pre>
glam2format fasta my_motif.glam2
</pre><pre>
glam2format msf my_motif.glam2
</pre>
</li>
<li>Use -o to write the output to a file rather than to the screen:
<pre>
glam2format -o my_motif.fa fasta my_motif.glam2
</pre><pre>
glam2format -o my_motif.msf msf my_motif.glam2
</pre>
</li>
<li>Use -c to make a compact alignment:
<pre>
glam2format -c fasta my_motif.glam2
</pre><pre>
glam2format -c msf my_motif.glam2
</pre>
By default, residues that are inserted between key positions are
written as unaligned with each other. This best reflects glam2's
intention, but it can make the alignment large and full of gaps. With
-c, inserted residues are written as arbitrarily aligned with each
other, just as they appear in the glam2 output.</li>
<li>Use -f to make a 'global' alignment by adding flanking sequences
from the original FASTA-format sequence file:
<pre>
glam2format -f my_seqs.fa fasta my_motif.glam2
</pre><pre>
glam2format -f my_seqs.fa msf my_motif.glam2
</pre>
The flanking sequences will be written as either unaligned with each
other or arbitrarily aligned, depending on the -c option. The
sequences should have unique names and their order should be
unchanged.</li>
</ul>
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