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<h1>glam2 Reference</h1>
<h2>Usage</h2>
<pre>
glam2 [options] alphabet my_seqs.fa
</pre>
<p>An alphabet other than p or n is interpreted as the name of an <a
href="alphabet.html">alphabet file</a>.</p>
<h2>Options that determine which alignments are possible</h2>
<dl>
<dt>-2</dt><dd>Search both strands.</dd>
<dt>-z</dt><dd>Specify the minimum number sequences that must
participate in the alignment. If greater than the number of input
sequences, then all the sequences must participate.</dd>
<dt>-a</dt><dd>Specify the minimum number of key positions (aligned
columns) in the alignment.</dd>
<dt>-b</dt><dd>Specify the maximum number of key positions (aligned
columns) in the alignment.</dd>
</dl>
<h2>Options that affect the scoring scheme</h2>
<p>These options specify parameters in the formula for calculating
alignment scores. See <a href="GLAM2_method.pdf">GLAM2 methods
(PDF)</a> for details.</p>
<dl>
<dt>-d</dt><dd>Specify a <a href="dirichlet.html">Dirichlet
mixture</a> file, which describes residues' tendencies to align with
one another.</dd>
<dt>-D</dt><dd>Specify the deletion pseudocount.</dd>
<dt>-E</dt><dd>Specify the 'no-deletion' pseudocount.</dd>
<dt>-I</dt><dd>Specify the insertion pseudocount.</dd>
<dt>-J</dt><dd>Specify the 'no-insertion' pseudocount.</dd>
<dt>-q</dt><dd>Specify the weight for generic versus
sequence-set-specific residue abundances. The residue abundances are
estimated by counting the residue types in all the input sequences,
and adding pseudocounts. The total number of pseudocounts is equal to
the alphabet size mutiplied by the -q parameter. The allocation of
pseudocounts among the residue types depends on the <a
href="alphabet.html">alphabet</a>.</dd>
</dl>
<h2>Options that affect the search algorithm</h2>
<p>glam2 uses a <a
href="http://en.wikipedia.org/wiki/Simulated_annealing">simulated
annealing</a> algorithm, with a temperature parameter. At high
temperatures, glam2 only slightly favours changes that increase the
alignment's score, and at low temperatures it strongly favours such
changes. Thus, at high temperatures the score will be optimized too
slowly, but at low temperatures the algorithm will get frozen in a
local optimum. The strategy, then, is to start with a high temperature
and reduce it as slowly as possible.</p>
<dl>
<dt>-r</dt><dd>Specify the number of alignment runs.</dd>
<dt>-n</dt><dd>Specify how many iterations should pass since the
highest-scoring alignment seen so far before ending each alignment
run.</dd>
<dt>-w</dt><dd>Specify the initial number of key positions (aligned
columns) in the alignment. If less than the minimum (-a) or greater
than the maximum (-b), it is increased to the minimum or reduced to
the maximum.</dd>
<dt>-t</dt><dd>Specify the initial temperature.</dd>
<dt>-c</dt><dd>Specify the cooling factor per n iterations. The
temperature is multiplied by a constant factor after each iteration,
such that after n iterations, it has dropped by this amount. 'n' is
the number specified with the -n option.</dd>
<dt>-u</dt><dd>Specify the minimum temperature. The temperature never
drops below this level, to avoid numerical problems.</dd>
<dt>-m</dt><dd>Specify the rate of column sampling relative to site
sampling. On each iteration, glam2 randomly decides to try either
realigning a sequence or adjusting an aligned column (key
position). This parameter sets the probabilities for this
decision.</dd>
<dt>-x</dt><dd>Specify the site sampling algorithm: 0=FAST, 1=SLOW,
2=FFT. See <a href="GLAM2_method.pdf">GLAM2 methods (PDF)</a> for
details. In summary, the FAST algorithm deviates slightly from the
strict definition of simulated annealing, but works well in
practice. The SLOW algorithm implements strict simulated annealing,
but is much slower, especially for longer sequences. The FFT algorithm
also implements strict simulated annealing, and has intermediate
speed, but carries greater risk of numerical roundoff error. In order
to use the FFT algorithm, it is necessary to install the <a
href="http://www.fftw.org/">FFTW library</a>, and re-compile glam2
with 'make glam2fft'.</dd>
<dt>-s</dt><dd>Specify the seed for pseudo-random number
generation. Change this to avoid getting identical results each time
the program is run.</dd>
</dl>
<h2>Cosmetic options</h2>
<dl>
<dt>-h</dt><dd>Show all options and their default settings.</dd>
<dt>-o</dt><dd>Specify an output file name.</dd>
<dt>-p</dt><dd>Print information about the algorithm's state before
each iteration. The following information is printed: the temperature,
the number of key positions in the alignment, the number of sequences
in the alignment, and the alignment's score. In addition, some
information about each move is printed: for site sampling moves, which
sequence is picked, and for column sampling moves, which column is
picked, whether or not it is deleted, and whether the direction is
left or right.</dd>
<h2>Warnings</h2>
<p>glam2 might occasionally issue this warning: 'accuracy loss due to
numeric underflow'. If this happens, its ability to optimise the
alignment may be harmed: see <a href="GLAM2_method.pdf">GLAM2 methods
(PDF)</a> for details. To fix this, try increasing -u, or possibly
decreasing -b. Increasing -u somewhat should be harmless, as long as
it stays well below 1.</p>
</dl>
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