~ubuntu-branches/ubuntu/feisty/amap-align/feisty

<para>On &debian; systems, the <command>amap</command> command has been renamed <command>amap-align</command> because there was already another tool called <command>amap</command> (which performs some computer network diagnostics)</para>

<para>AMAP is a tool to perform multiple alignment of peptidic sequences. It utilizes posterior decoding, and a sequence-annealing alignment, instead of the traditional progressive alignment method. It is the only alignment program that allows to control the sensitivity / specificity tradeoff. It is based on the ProbCons source code, but uses alignment metric accuracy and eliminates the consistency transformation.</para>

<para>In its default configuration, AMAP is tuned to maximize the expected Alignment Metric Accuracy (AMA) score - a new alignment accuracy measure, based on a metric for the multiple-alignment space, which integrates sensitivity and specificity into a single balanced measure. AMA is defined as the fraction of correctly aligned residues (either to another residue or to a gap) out of the total number of residues in all the sequences.</para>

<para><command>&dhpackage;</command> aligns sequences provided in MFA format. This format consists of multiple sequences. Each sequence in MFA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (<quote>></quote>) symbol in the first column.</para>

</refsect1>

<title>OPTIONS</title>

<term><option>-clustalw</option>

</term>

<para>use CLUSTALW output format instead of MFA</para>

</listitem>

</varlistentry>

<option>--consistency</option> <varname>REPS</varname>

</term>

</listitem>

</varlistentry>

<option>--iterative-refinement</option> <varname>REPS</varname>

</term>

</listitem>

</varlistentry>

<option>--pre-training</option> <varname>REPS</varname>

</term>

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</listitem>

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</varlistentry>

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<term>

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<option>-pairs</option>

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</term>

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<para>generate all-pairs pairwise alignments</para>

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</listitem>

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</varlistentry>

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<term>

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<option>-viterbi</option>

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</term>

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<para>use Viterbi algorithm to generate all pairs (automatically enables <option>-pairs</option>)</para>

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</listitem>

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</varlistentry>

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<term>

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<option>--verbose</option>

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</term>

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<para>Report progress while aligning (default: off)</para>

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</listitem>

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</varlistentry>

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<term><option>-annot</option> <filename>FILENAME</filename> </term>

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<para>write annotation for multiple alignment to <filename>FILENAME</filename></para>

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</listitem>

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</varlistentry>

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<option>--train</option> <filename>FILENAME</filename>

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</term>

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<para>compute EM transition probabilities, store in <filename>FILENAME</filename> (default: no training)</para>

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</listitem>

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</varlistentry>

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<option>--emissions</option>

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</term>

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<para>also reestimate emission probabilities (default: off)</para>

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</listitem>

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</varlistentry>

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<option>--paramfile</option> <filename>FILENAME</filename>

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</term>

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<para>read parameters from <filename>FILENAME</filename> (default: )</para>

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</listitem>

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</varlistentry>

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<option>--alignment-order</option>

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</term>

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<para>print sequences in alignment order rather than input order (default: off)</para>

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</listitem>

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</varlistentry>

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<option>--gap-factor</option>

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</term>

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<para>use <varname>GF</varname> as the gap-factor parameter, set to 0 for best sensitivity, higher values for better specificity (default: 0.5)</para>

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</listitem>

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</varlistentry>

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<option>--edge-weight-threshold</option>

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</term>

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<para>stop the sequence annealing process when best edge has lower weight than <varname>W</varname>, set to 0 for best sensitivity, higher values for better specificity (default: 0)</para>

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</listitem>

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</varlistentry>

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<option>--progressive</option>

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</term>

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<para>use progressive alignment instead of sequence annealing alignment (default: off)</para>

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</listitem>

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</varlistentry>

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<term><option>-noreorder</option>

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<option>--no-edge-reordering</option>

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</term>

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<para>disable reordering of edges during sequence annealing alignment (default: off)</para>

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</listitem>

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</varlistentry>

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<term><option>-maxstep</option>

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<option>--use-max-stepsize</option>

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</term>

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<para>use maximum improvement step size instead of tGf edge ranking (default: off)</para>

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</listitem>

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</varlistentry>

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<term><option>-print</option>

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<option>--print-posteriors</option>

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</term>

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<para>only print the posterior probability matrices (default: off)</para>

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</listitem>

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</varlistentry>

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</variablelist>

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</refsect1>

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<para>The current version of AMAP uses the PROBCONS 1.09 code base for some of the input/output procedures, and for the calculation of posterior probabilities (see PROBCONS.README in <filename>/usr/share/doc/amap-align/</filename>). Future releases might implement the algorithm using a new independent code base. On &debian; systems, PROBCONS is available in the probcons package.</para>

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</refsect1>

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<title>REFERENCES</title>

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<para>

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For more details on AMAP and AMA, see Schwartz, Ariel S., Myers, Eugene W., and Pachter, Lior. Alignment Metric Accuracy (Submitted for publication). For more details on sequence-annealing, see Schwartz, Ariel S. and Pachter, Lior. Multiple Alignment by Sequence Annealing (Submitted for publication).

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</para>

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<para>

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PROBCONS was published in Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340.

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</para>

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</refsect1>

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<title>AUTHORS</title>

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<listitem><para>PROBCONS was written by Chuong Do.</para></listitem>

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<listitem><para>AMAP algorithm implemented by Ariel Schwartz (<email>sariel@cs.berkeley.edu</email>).</para></listitem>

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<listitem><para>This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others).</para></listitem>

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</itemizedlist>

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</refsect1>

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<title>LICENCE</title>

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<para>

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AMAP comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome to redistribute it under certain conditions. See the files README and README.PROBCONS for details.

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</para>

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<para>This manpage is hereby placed in the public domain.</para>

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</refsect1>

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</refentry>

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