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7 Uses of Interface compbio.engine.client.PipedExecutable
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42 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
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84 <B>Uses of Interface<br>compbio.engine.client.PipedExecutable</B></H2>
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89 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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90 Packages that use <A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A></FONT></TH>
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92 <TR BGCOLOR="white" CLASS="TableRowColor">
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93 <TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>
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94 <TD> </TD>
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96 <TR BGCOLOR="white" CLASS="TableRowColor">
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97 <TD><A HREF="#compbio.runner.disorder"><B>compbio.runner.disorder</B></A></TD>
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98 <TD> </TD>
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100 <TR BGCOLOR="white" CLASS="TableRowColor">
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101 <TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>
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102 <TD>Wrappers for native executables for multiple sequence alignment (msa) </TD>
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107 <A NAME="compbio.engine.client"><!-- --></A>
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108 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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109 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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110 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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111 Uses of <A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A> in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>
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117 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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118 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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119 <TH ALIGN="left" COLSPAN="2">Subinterfaces of <A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A> in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>
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121 <TR BGCOLOR="white" CLASS="TableRowColor">
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122 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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123 <CODE> interface</CODE></FONT></TD>
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124 <TD><CODE><B><A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable<T></A></B></CODE>
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127 </TD>
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133 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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134 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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135 <TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that implement <A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A></FONT></TH>
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137 <TR BGCOLOR="white" CLASS="TableRowColor">
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138 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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139 <CODE> class</CODE></FONT></TD>
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140 <TD><CODE><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable<T></A></B></CODE>
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143 </TD>
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148 <A NAME="compbio.runner.disorder"><!-- --></A>
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149 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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150 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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151 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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152 Uses of <A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A> in <A HREF="../../../../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A></FONT></TH>
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158 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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159 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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160 <TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A> that implement <A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A></FONT></TH>
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162 <TR BGCOLOR="white" CLASS="TableRowColor">
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163 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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164 <CODE> class</CODE></FONT></TD>
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165 <TD><CODE><B><A HREF="../../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A></B></CODE>
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168 DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops
169 fold_rem465 sequence_file print
171 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out'
173 This version of DisEMBL is 1.4 (latest available for download in Feb 2011)
174 capable of outputting raw values
176 The values of the parameters are hard coded in DisEMBL.py script.</TD>
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178 <TR BGCOLOR="white" CLASS="TableRowColor">
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179 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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180 <CODE> class</CODE></FONT></TD>
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181 <TD><CODE><B><A HREF="../../../../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A></B></CODE>
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184 ./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame
186 FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file'
187 Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file'
189 Hard-coded values are 10 15 74 4 5.</TD>
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194 <A NAME="compbio.runner.msa"><!-- --></A>
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195 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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196 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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197 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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198 Uses of <A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A> in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>
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204 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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205 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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206 <TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that implement <A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A></FONT></TH>
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208 <TR BGCOLOR="white" CLASS="TableRowColor">
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209 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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210 <CODE> class</CODE></FONT></TD>
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211 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></B></CODE>
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214 </TD>
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216 <TR BGCOLOR="white" CLASS="TableRowColor">
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217 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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218 <CODE> class</CODE></FONT></TD>
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219 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></B></CODE>
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222 </TD>
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224 <TR BGCOLOR="white" CLASS="TableRowColor">
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225 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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226 <CODE> class</CODE></FONT></TD>
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227 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></B></CODE>
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