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<?xml version='1.0' encoding='ISO-8859-1'?>
<?xml-stylesheet type="text/xsl"
href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.2//EN"
"/usr/share/xml/docbook/schema/dtd/4.4/docbookx.dtd" [
<!ENTITY dhfirstname "Charles">
<!ENTITY dhsurname "Plessy">
<!ENTITY dhusername "&dhfirstname; &dhsurname;">
<!ENTITY dhdate "2007-04-04">
<!ENTITY dhsection "1">
<!ENTITY dhemail "charles-debian-nospam@plessy.org">
<!ENTITY dhucpackage "PC-COMPARE">
<!ENTITY dhpackage "pc-compare">
<!ENTITY dhrelease "1.12">
<!ENTITY dhproduct "&dhpackage;">
<!ENTITY dhtitle "Probcons Manual">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
]>
<refentry>
<refentryinfo>
<title>&dhtitle;</title>
<productname>&dhpackage;</productname>
<releaseinfo role="version">&dhrelease;</releaseinfo>
<date>&dhdate;</date>
<authorgroup>
<author>
<firstname>Chuong</firstname>
<surname>Do</surname>
<contrib>Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University.</contrib>
<address>
<email>chuongdo@cs.stanford.edu</email>
</address>
</author>
<author>
<firstname>&dhfirstname;</firstname>
<surname>&dhsurname;</surname>
<contrib>Wrote this manpage in DocBook XML for the Debian distribution.</contrib>
<address>
<email>&dhemail;</email>
</address>
</author>
</authorgroup>
<!--<copyright>
<year>2004</year>
<year>2005</year>
<year>2006</year>
<year>2007</year>
<holder>Chuong Do</holder>
</copyright>
<copyright>
<year>2006</year>
<year>2007</year>
<holder>&dhusername;</holder>
</copyright>--><!-- Public domain: no copyright -->
<legalnotice>
<para>This program and its manpage are in the public domain.</para>
</legalnotice>
</refentryinfo>
<refmeta>
<refentrytitle>&dhucpackage;</refentrytitle>
<manvolnum>&dhsection;</manvolnum>
</refmeta>
<refnamediv>
<refname>&dhpackage;</refname>
<refpurpose>Program for scoring alignments
according to a reference alignment with respect to
sum-of-pairs and column scores.</refpurpose>
</refnamediv>
<refsynopsisdiv>
<cmdsynopsis>
<command>&dhpackage;</command>
<arg><replaceable>TEST_ALIGNMENT</replaceable></arg>
<arg><replaceable>REFERENCE_ALIGNMENT</replaceable></arg>
<arg choice="opt"><replaceable>BALIBASE_ANNOT_FILE</replaceable></arg>
<arg choice="opt"><option>-col</option></arg>
<arg choice="opt"><option>-core</option></arg>
<arg choice="opt"><option>-caps</option></arg>
<arg choice="opt">
<option>-annot <replaceable>FILENAME</replaceable></option>
</arg>
</cmdsynopsis>
</refsynopsisdiv>
<refsect1>
<title>NOTE</title>
<para>&dhpackage; is named <filename>compare</filename> in the original sources, but has been remamed to avoid collision with other program names.</para>
</refsect1>
<refsect1>
<title>SEE ALSO</title>
<para>
<citerefentry>
<refentrytitle>pc-makegnufile</refentrytitle>
<manvolnum>1</manvolnum>
</citerefentry>,
<citerefentry>
<refentrytitle>pc-project</refentrytitle>
<manvolnum>1</manvolnum>
</citerefentry>,from the probcons-extra package, and
<citerefentry>
<refentrytitle>probcons</refentrytitle>
<manvolnum>1</manvolnum>
</citerefentry> and
<citerefentry>
<refentrytitle>probcons-RNA</refentrytitle>
<manvolnum>1</manvolnum>
</citerefentry> from the probcons package.</para>
</refsect1>
<refsect1>
<title>REFERENCE</title>
<para>Please cite 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.</para>
</refsect1>
</refentry>
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