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+Package compbio.pipeline._jpred\r
+</H2>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Class Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/BlastBlastComparator.html" title="class in compbio.pipeline._jpred">BlastBlastComparator</A></B></TD>\r
+<TD> </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/BlastHmmerComparator.html" title="class in compbio.pipeline._jpred">BlastHmmerComparator</A></B></TD>\r
+<TD> </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/BlastParser.html" title="class in compbio.pipeline._jpred">BlastParser</A></B></TD>\r
+<TD> </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/Hit.html" title="class in compbio.pipeline._jpred">Hit</A></B></TD>\r
+<TD> </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/Hit.EvalueComporator.html" title="class in compbio.pipeline._jpred">Hit.EvalueComporator</A></B></TD>\r
+<TD> </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/Hit.NumberComporator.html" title="class in compbio.pipeline._jpred">Hit.NumberComporator</A></B></TD>\r
+<TD> </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/JackHmmerHitParser.html" title="class in compbio.pipeline._jpred">JackHmmerHitParser</A></B></TD>\r
+<TD>Parser for the following files:</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/Jpred4.html" title="class in compbio.pipeline._jpred">Jpred4</A></B></TD>\r
+<TD>jpred --sequence <fasta file> OR --alignment <clustalW alignment> [--db
+ <database>] [--pred-nohits] [--logLevel=(ERROR|INFO|DEBUG)] [--help]
+
+ jpred4 --sequence <fasta file> The path to the sequence (in FASTA format) you
+ want to predict OR
+
+ [--alignment <clustalW alignment>] The alignment which to use for prediction
+
+ [--profile=<path to HMM profile>]
+
+ [--db <database>] Database to use for PSI-BLAST querying.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/Pairwise.html" title="class in compbio.pipeline._jpred">Pairwise</A></B></TD>\r
+<TD> </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/PScore.html" title="class in compbio.pipeline._jpred">PScore</A></B></TD>\r
+<TD> </TD>\r
+</TR>\r
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