#aacon.cluster.settings = -q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00\r
\r
###########################################################################################\r
-# MAFFT CONFIGURATION #\r
+# JPRED CONFIGURATION #\r
###########################################################################################\r
local.jpred.bin = binaries/src/jpred/jpred.pl\r
#cluster.jpred.bin = /home/jabaws/binaries/src/jpred/jpred.pl\r
### This parameters specifies the directory where the matrices files are stored\r
jpred.presets.file = conf/settings/JpredPresets.xml\r
jpred.parameters.file = conf/settings/JpredParameters.xml\r
-#jpred.limits.file = conf/settings/JpredLimits.xml\r
+jpred.limits.file = conf/settings/JpredLimits.xml\r
+jpred.cluster.cpunum = 4\r
#jpred.cluster.settings = -l h_cpu=24:00:00 -l ram=6000M\r
<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
<limits>\r
- <runnerClassName>compbio.runner.conservation.AACon</runnerClassName>\r
- <limit isDefault="true">\r
- <seqNumber>5000</seqNumber>\r
- <seqLength>1000</seqLength>\r
- </limit>\r
- <limit isDefault="false">\r
- <preset># LocalEngineExecutionLimit #</preset>\r
- <seqNumber>200</seqNumber>\r
- <seqLength>400</seqLength>\r
- </limit>\r
-\r
- <!-- Limits for presets -->\r
- <limit isDefault="false">\r
- <preset>Quick conservation</preset>\r
- <seqNumber>10000</seqNumber>\r
- <seqLength>10000</seqLength>\r
- </limit>\r
- <limit isDefault="false">\r
- <preset>Slow conservation</preset>\r
- <seqNumber>2000</seqNumber>\r
- <seqLength>1000</seqLength>\r
- </limit>\r
- <limit isDefault="false">\r
- <preset>Complete conservation</preset>\r
- <seqNumber>2000</seqNumber>\r
- <seqLength>1000</seqLength>\r
- </limit>\r
+ <runnerClassName>compbio.runner.conservation.AACon</runnerClassName>\r
+ <limit isDefault="true">\r
+ <seqNumber>5000</seqNumber>\r
+ <seqLength>1000</seqLength>\r
+ </limit>\r
+ <limit isDefault="false">\r
+ <preset># LocalEngineExecutionLimit #</preset>\r
+ <seqNumber>200</seqNumber>\r
+ <seqLength>400</seqLength>\r
+ </limit>\r
\r
+ <!-- Limits for presets -->\r
+ <limit isDefault="false">\r
+ <preset>Quick conservation</preset>\r
+ <seqNumber>10000</seqNumber>\r
+ <seqLength>10000</seqLength>\r
+ </limit>\r
+ <limit isDefault="false">\r
+ <preset>Slow conservation</preset>\r
+ <seqNumber>2000</seqNumber>\r
+ <seqLength>1000</seqLength>\r
+ </limit>\r
+ <limit isDefault="false">\r
+ <preset>Complete conservation</preset>\r
+ <seqNumber>2000</seqNumber>\r
+ <seqLength>1000</seqLength>\r
+ </limit>\r
</limits>\r
<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
<runnerConfig>\r
- <runnerClassName>compbio.runner.conservation.AACon</runnerClassName>\r
- <options>\r
- <name>Normalize</name>\r
- <description>\r
- Normalize the results. Normalized results have values between 0 and 1. Please note however, \r
- that some results cannot be normalized. In such a case, the system returns not \r
- normalized value. The following formula is used for normalization n = (d - dmin)/(dmax - dmin)\r
- Negative results first converted to positive by adding a greatest absolute result value.\r
- </description>\r
- <optionNames>-n</optionNames>\r
- <defaultValue>-n</defaultValue>\r
- <furtherDetails>prog_docs/aacon.txt</furtherDetails>\r
- </options>\r
- <options><name>KABAT</name><description></description><optionNames>-m=KABAT</optionNames><furtherDetails>prog_docs/aacon.txt#KABAT</furtherDetails></options>\r
- <options><name>JORES</name><description></description><optionNames>-m=JORES</optionNames><furtherDetails>prog_docs/aacon.txt#JORES</furtherDetails></options>\r
- <options><name>SCHNEIDER</name><description></description><optionNames>-m=SCHNEIDER</optionNames><furtherDetails>prog_docs/aacon.txt#SCHNEIDER</furtherDetails></options>\r
- <options><name>SHENKIN</name><description></description><optionNames>-m=SHENKIN</optionNames><furtherDetails>prog_docs/aacon.txt#SHENKIN</furtherDetails><defaultValue>-m=SHENKIN</defaultValue></options>\r
- <options><name>GERSTEIN</name><description></description><optionNames>-m=GERSTEIN</optionNames><furtherDetails>prog_docs/aacon.txt#GERSTEIN</furtherDetails></options>\r
- <options><name>TAYLOR_GAPS</name><description></description><optionNames>-m=TAYLOR_GAPS</optionNames><furtherDetails>prog_docs/aacon.txt#TAYLOR_GAPS</furtherDetails></options>\r
- <options><name>TAYLOR_NO_GAPS</name><description></description><optionNames>-m=TAYLOR_NO_GAPS</optionNames><furtherDetails>prog_docs/aacon.txt#TAYLOR_NO_GAPS</furtherDetails></options> \r
- <options><name>ZVELIBIL</name><description></description><optionNames>-m=ZVELIBIL</optionNames><furtherDetails>prog_docs/aacon.txt#ZVELIBIL</furtherDetails></options>\r
- <options><name>KARLIN</name><description></description><optionNames>-m=KARLIN</optionNames><furtherDetails>prog_docs/aacon.txt#KARLIN</furtherDetails></options>\r
- <options><name>ARMON</name><description></description><optionNames>-m=ARMON</optionNames><furtherDetails>prog_docs/aacon.txt#ARMON</furtherDetails></options>\r
- <options><name>THOMPSON</name><description></description><optionNames>-m=THOMPSON</optionNames><furtherDetails>prog_docs/aacon.txt#THOMPSON</furtherDetails></options>\r
- <options><name>NOT_LANCET</name><description></description><optionNames>-m=NOT_LANCET</optionNames><furtherDetails>prog_docs/aacon.txt#NOT_LANCET</furtherDetails></options>\r
- <options><name>MIRNY</name><description></description><optionNames>-m=MIRNY</optionNames><furtherDetails>prog_docs/aacon.txt#MIRNY</furtherDetails></options>\r
- <options><name>WILLIAMSON</name><description></description><optionNames>-m=WILLIAMSON</optionNames><furtherDetails>prog_docs/aacon.txt#WILLIAMSON</furtherDetails></options> \r
- <options><name>LANDGRAF</name><description></description><optionNames>-m=LANDGRAF</optionNames><furtherDetails>prog_docs/aacon.txt#LANDGRAF</furtherDetails></options>\r
- <options><name>SANDER</name><description></description><optionNames>-m=SANDER</optionNames><furtherDetails>prog_docs/aacon.txt#SANDER</furtherDetails></options>\r
- <options><name>VALDAR</name><description></description><optionNames>-m=VALDAR</optionNames><furtherDetails>prog_docs/aacon.txt#VALDAR</furtherDetails></options>\r
- <options><name>SMERFS</name><description></description><optionNames>-m=SMERFS</optionNames><furtherDetails>prog_docs/aacon.txt#SMERFS</furtherDetails></options>\r
-\r
- <prmSeparator>=</prmSeparator>\r
- <parameters>\r
- <name>SMERFS Window Width</name>\r
- <description>The width of the window for SMERFS. Optional, defaults to 7</description>\r
- <optionNames>-smerfsWW</optionNames>\r
- <furtherDetails>prog_docs/aacon.txt</furtherDetails>\r
- <defaultValue>7</defaultValue>\r
- <validValue>\r
- <type>Integer</type>\r
- <min>3</min>\r
- <max>100</max>\r
- </validValue>\r
- </parameters>\r
-\r
- <parameters>\r
- <name>SMERFS Column Scoring Method</name>\r
- <description>SMERFS Column Score algorithm defines the window scores to \r
- columns allocation, two methods are possible: MID_SCORE - gives the window score to the middle column\r
- MAX_SCORE - gives the column the highest score of all the windows it belongs to. Optional defaults to MID_SCORE. </description>\r
- <optionNames>-smerfsCS</optionNames>\r
- <furtherDetails>prog_docs/aacon.txt</furtherDetails>\r
- <defaultValue>MID_SCORE</defaultValue>\r
- <possibleValues>MAX_SCORE</possibleValues>\r
- <possibleValues>MID_SCORE</possibleValues>\r
- </parameters>\r
-\r
- <parameters>\r
- <name>SMERFS Gap Threshhold</name>\r
- <description>a gap percentage cutoff - a float greater than 0 and smaller or equal 1. Optional defaults to 0.1</description>\r
- <optionNames>-smerfsGT</optionNames>\r
- <furtherDetails>prog_docs/aacon.txt</furtherDetails>\r
- <defaultValue>0.1</defaultValue>\r
- <validValue>\r
- <type>Float</type>\r
+ <runnerClassName>compbio.runner.conservation.AACon</runnerClassName>\r
+\r
+ <options>\r
+ <name>Normalize</name>\r
+ <description>\r
+ Normalize the results. Normalized results have values between 0 and 1. Please note however, \r
+ that some results cannot be normalized. In such a case, the system returns not \r
+ normalized value. The following formula is used for normalization n = (d - dmin)/(dmax - dmin)\r
+ Negative results first converted to positive by adding a greatest absolute result value.\r
+ </description>\r
+ <optionNames>-n</optionNames>\r
+ <defaultValue>-n</defaultValue>\r
+ <furtherDetails>prog_docs/aacon.txt</furtherDetails>\r
+ </options>\r
+\r
+ <options>\r
+ <name>SHENKIN</name>\r
+ <description></description>\r
+ <optionNames>-m=SHENKIN</optionNames>\r
+ <furtherDetails>prog_docs/aacon.txt#SHENKIN</furtherDetails>\r
+ <defaultValue>-m=SHENKIN</defaultValue>\r
+ </options>\r
+\r
+ <options>\r
+ <name>KABAT</name>\r
+ <description></description>\r
+ <optionNames>-m=KABAT</optionNames>\r
+ <furtherDetails>prog_docs/aacon.txt#KABAT</furtherDetails>\r
+ </options>\r
+\r
+ <options>\r
+ <name>JORES</name>\r
+ <description></description>\r
+ <optionNames>-m=JORES</optionNames>\r
+ <furtherDetails>prog_docs/aacon.txt#JORES</furtherDetails>\r
+ </options>\r
+\r
+ <options>\r
+ <name>SCHNEIDER</name>\r
+ <description></description>\r
+ <optionNames>-m=SCHNEIDER</optionNames>\r
+ <furtherDetails>prog_docs/aacon.txt#SCHNEIDER</furtherDetails>\r
+ </options>\r
+\r
+ <options>\r
+ <name>GERSTEIN</name>\r
+ <description></description>\r
+ <optionNames>-m=GERSTEIN</optionNames>\r
+ <furtherDetails>prog_docs/aacon.txt#GERSTEIN</furtherDetails>\r
+ </options>\r
+\r
+ <options>\r
+ <name>TAYLOR_GAPS</name>\r
+ <description></description>\r
+ <optionNames>-m=TAYLOR_GAPS</optionNames>\r
+ <furtherDetails>prog_docs/aacon.txt#TAYLOR_GAPS</furtherDetails>\r
+ </options>\r
+\r
+ <options>\r
+ <name>TAYLOR_NO_GAPS</name>\r
+ <description></description>\r
+ <optionNames>-m=TAYLOR_NO_GAPS</optionNames>\r
+ <furtherDetails>prog_docs/aacon.txt#TAYLOR_NO_GAPS</furtherDetails>\r
+ </options> \r
+ <options>\r
+ <name>ZVELIBIL</name>\r
+ <description></description>\r
+ <optionNames>-m=ZVELIBIL</optionNames>\r
+ <furtherDetails>prog_docs/aacon.txt#ZVELIBIL</furtherDetails>\r
+ </options>\r
+\r
+ <options>\r
+ <name>KARLIN</name>\r
+ <description></description>\r
+ <optionNames>-m=KARLIN</optionNames>\r
+ <furtherDetails>prog_docs/aacon.txt#KARLIN</furtherDetails>\r
+ </options>\r
+\r
+ <options>\r
+ <name>ARMON</name>\r
+ <description></description>\r
+ <optionNames>-m=ARMON</optionNames>\r
+ <furtherDetails>prog_docs/aacon.txt#ARMON</furtherDetails>\r
+ </options>\r
+\r
+ <options>\r
+ <name>THOMPSON</name>\r
+ <description></description>\r
+ <optionNames>-m=THOMPSON</optionNames>\r
+ <furtherDetails>prog_docs/aacon.txt#THOMPSON</furtherDetails>\r
+ </options>\r
+\r
+ <options>\r
+ <name>NOT_LANCET</name>\r
+ <description></description>\r
+ <optionNames>-m=NOT_LANCET</optionNames>\r
+ <furtherDetails>prog_docs/aacon.txt#NOT_LANCET</furtherDetails>\r
+ </options>\r
+\r
+ <options>\r
+ <name>MIRNY</name>\r
+ <description></description>\r
+ <optionNames>-m=MIRNY</optionNames>\r
+ <furtherDetails>prog_docs/aacon.txt#MIRNY</furtherDetails>\r
+ </options>\r
+\r
+ <options>\r
+ <name>WILLIAMSON</name>\r
+ <description></description>\r
+ <optionNames>-m=WILLIAMSON</optionNames>\r
+ <furtherDetails>prog_docs/aacon.txt#WILLIAMSON</furtherDetails>\r
+ </options> \r
+ <options>\r
+ <name>LANDGRAF</name>\r
+ <description></description>\r
+ <optionNames>-m=LANDGRAF</optionNames>\r
+ <furtherDetails>prog_docs/aacon.txt#LANDGRAF</furtherDetails>\r
+ </options>\r
+\r
+ <options>\r
+ <name>SANDER</name>\r
+ <description></description>\r
+ <optionNames>-m=SANDER</optionNames>\r
+ <furtherDetails>prog_docs/aacon.txt#SANDER</furtherDetails>\r
+ </options>\r
+\r
+ <options>\r
+ <name>VALDAR</name>\r
+ <description></description>\r
+ <optionNames>-m=VALDAR</optionNames>\r
+ <furtherDetails>prog_docs/aacon.txt#VALDAR</furtherDetails>\r
+ </options>\r
+\r
+ <options>\r
+ <name>SMERFS</name>\r
+ <description></description>\r
+ <optionNames>-m=SMERFS</optionNames>\r
+ <furtherDetails>prog_docs/aacon.txt#SMERFS</furtherDetails>\r
+ </options>\r
+\r
+ <prmSeparator>=</prmSeparator>\r
+\r
+ <parameters>\r
+ <name>SMERFS Window Width</name>\r
+ <description>\r
+ The width of the window for SMERFS. Optional, defaults to 7\r
+ </description>\r
+ <optionNames>-smerfsWW</optionNames>\r
+ <furtherDetails>prog_docs/aacon.txt</furtherDetails>\r
+ <defaultValue>7</defaultValue>\r
+ <validValue>\r
+ <type>Integer</type>\r
+ <min>3</min>\r
+ <max>100</max>\r
+ </validValue>\r
+ </parameters>\r
+\r
+ <parameters>\r
+ <name>SMERFS Column Scoring Method</name>\r
+ <description>\r
+ SMERFS Column Score algorithm defines the window scores to columns allocation, \r
+ two methods are possible: MID_SCORE - gives the window score to the middle column\r
+ MAX_SCORE - gives the column the highest score of all the windows it belongs to. \r
+ Optional defaults to MID_SCORE.\r
+ </description>\r
+ <optionNames>-smerfsCS</optionNames>\r
+ <furtherDetails>prog_docs/aacon.txt</furtherDetails>\r
+ <defaultValue>MID_SCORE</defaultValue>\r
+ <possibleValues>MAX_SCORE</possibleValues>\r
+ <possibleValues>MID_SCORE</possibleValues>\r
+ </parameters>\r
+\r
+ <parameters>\r
+ <name>SMERFS Gap Threshhold</name>\r
+ <description>\r
+ a gap percentage cutoff - a float greater than 0 and smaller or equal 1.\r
+ Optional defaults to 0.1\r
+ </description>\r
+ <optionNames>-smerfsGT</optionNames>\r
+ <furtherDetails>prog_docs/aacon.txt</furtherDetails>\r
+ <defaultValue>0.1</defaultValue>\r
+ <validValue>\r
+ <type>Float</type>\r
<min>0.001</min>\r
<max>1</max>\r
</validValue>\r
- </parameters>\r
+ </parameters>\r
\r
</runnerConfig>\r
<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
<presets>\r
-<runnerClassName>compbio.runner.conservation.AACon</runnerClassName>\r
- <preset>\r
- <name>Quick conservation</name>\r
- <description>Collection of fast conservation methods</description>\r
- <optlist>\r
- <option>-m=KABAT</option><option>-m=JORES</option><option>-m=SCHNEIDER</option><option>-m=SHENKIN</option><option>-m=GERSTEIN</option><option>-m=TAYLOR_GAPS</option><option>-m=TAYLOR_NO_GAPS</option><option>-m=ZVELIBIL</option><option>-m=ARMON</option><option>-m=THOMPSON</option><option>-m=NOT_LANCET</option><option>-m=MIRNY</option><option>-m=WILLIAMSON</option>\r
- </optlist>\r
- </preset>\r
- <preset>\r
- <name>Slow conservation</name>\r
- <description>Collection of most expensive (slow) conservation methods</description>\r
- <optlist>\r
- <option>-m=LANDGRAF</option><option>-m=KARLIN</option><option>-m=SANDER</option><option>-m=VALDAR</option><option>-m=SMERFS</option>\r
- </optlist>\r
- </preset>\r
- <preset>\r
- <name>Complete conservation</name>\r
- <description>Calculate conservation with all supported methods</description>\r
- <optlist>\r
- <option>-m=KABAT</option><option>-m=JORES</option><option>-m=SCHNEIDER</option><option>-m=SHENKIN</option><option>-m=GERSTEIN</option><option>-m=TAYLOR_GAPS</option><option>-m=TAYLOR_NO_GAPS</option><option>-m=ZVELIBIL</option><option>-m=ARMON</option><option>-m=THOMPSON</option><option>-m=NOT_LANCET</option><option>-m=MIRNY</option><option>-m=WILLIAMSON</option><option>-m=LANDGRAF</option><option>-m=KARLIN</option><option>-m=SANDER</option><option>-m=VALDAR</option><option>-m=SMERFS</option>\r
- </optlist>\r
- </preset>\r
+ <runnerClassName>compbio.runner.conservation.AACon</runnerClassName>\r
+ <preset>\r
+ <name>Quick conservation</name>\r
+ <description>\r
+ Collection of fast conservation methods\r
+ </description>\r
+ <optlist>\r
+ <option>-m=KABAT</option>\r
+ <option>-m=JORES</option>\r
+ <option>-m=SCHNEIDER</option>\r
+ <option>-m=SHENKIN</option>\r
+ <option>-m=GERSTEIN</option>\r
+ <option>-m=TAYLOR_GAPS</option>\r
+ <option>-m=TAYLOR_NO_GAPS</option>\r
+ <option>-m=ZVELIBIL</option>\r
+ <option>-m=ARMON</option>\r
+ <option>-m=THOMPSON</option>\r
+ <option>-m=NOT_LANCET</option>\r
+ <option>-m=MIRNY</option>\r
+ <option>-m=WILLIAMSON</option>\r
+ </optlist>\r
+ </preset>\r
+\r
+ <preset>\r
+ <name>Slow conservation</name>\r
+ <description>\r
+ Collection of most expensive (slow) conservation methods\r
+ </description>\r
+ <optlist>\r
+ <option>-m=LANDGRAF</option>\r
+ <option>-m=KARLIN</option>\r
+ <option>-m=SANDER</option>\r
+ <option>-m=VALDAR</option>\r
+ <option>-m=SMERFS</option>\r
+ </optlist>\r
+ </preset>\r
+\r
+ <preset>\r
+ <name>Complete conservation</name>\r
+ <description>\r
+ Calculate conservation with all supported methods\r
+ </description>\r
+ <optlist>\r
+ <option>-m=KABAT</option>\r
+ <option>-m=JORES</option>\r
+ <option>-m=SCHNEIDER</option>\r
+ <option>-m=SHENKIN</option>\r
+ <option>-m=GERSTEIN</option>\r
+ <option>-m=TAYLOR_GAPS</option>\r
+ <option>-m=TAYLOR_NO_GAPS</option>\r
+ <option>-m=ZVELIBIL</option>\r
+ <option>-m=ARMON</option>\r
+ <option>-m=THOMPSON</option>\r
+ <option>-m=NOT_LANCET</option>\r
+ <option>-m=MIRNY</option>\r
+ <option>-m=WILLIAMSON</option>\r
+ <option>-m=LANDGRAF</option>\r
+ <option>-m=KARLIN</option>\r
+ <option>-m=SANDER</option>\r
+ <option>-m=VALDAR</option>\r
+ <option>-m=SMERFS</option>\r
+ </optlist>\r
+ </preset>\r
</presets>\r
<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
<limits>\r
- <runnerClassName>compbio.runner.clustal.ClustalW</runnerClassName>\r
- <limit isDefault="true">\r
- <seqNumber>1000</seqNumber>\r
- <seqLength>1000</seqLength>\r
- </limit>\r
- <limit isDefault="false">\r
- <preset># LocalEngineExecutionLimit #</preset>\r
- <seqNumber>30</seqNumber>\r
- <seqLength>500</seqLength>\r
- </limit>\r
-\r
- <!-- Limits for presets -->\r
- <limit isDefault="false">\r
- <preset>Disable gap weighting (Speed-oriented)</preset>\r
- <seqNumber>1000</seqNumber>\r
- <seqLength>3000</seqLength>\r
- </limit>\r
+ <runnerClassName>compbio.runner.msa.ClustalW</runnerClassName>\r
+ <limit isDefault="true">\r
+ <seqNumber>1000</seqNumber>\r
+ <seqLength>1000</seqLength>\r
+ </limit>\r
+ <limit isDefault="false">\r
+ <preset># LocalEngineExecutionLimit #</preset>\r
+ <seqNumber>30</seqNumber>\r
+ <seqLength>500</seqLength>\r
+ </limit>\r
\r
+ <!-- Limits for presets -->\r
+ <limit isDefault="false">\r
+ <preset>Disable gap weighting (Speed-oriented)</preset>\r
+ <seqNumber>1000</seqNumber>\r
+ <seqLength>3000</seqLength>\r
+ </limit>\r
</limits>\r
<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
<runnerConfig>\r
- <runnerClassName>compbio.runner.clustal.ClustalW</runnerClassName>\r
+ <runnerClassName>compbio.runner.msa.ClustalW</runnerClassName>\r
+\r
<options>\r
<name>NOPGAP</name>\r
<description>Residue-specific gaps off</description>\r
<optionNames>-NOPGAP</optionNames>\r
<furtherDetails>prog_docs/clustalw.txt</furtherDetails>\r
</options>\r
+\r
<options>\r
<name>No transition weighting</name>\r
<description>Disable sequence weighting</description>\r
<optionNames>-NOWEIGHTS</optionNames>\r
<furtherDetails>prog_docs/clustalw.txt</furtherDetails>\r
</options>\r
+\r
<options>\r
<name>NOHGAP</name>\r
<description>Hydrophilic gaps off</description>\r
<optionNames>-NOHGAP</optionNames>\r
<furtherDetails>prog_docs/clustalw.txt</furtherDetails>\r
</options>\r
+\r
<prmSeparator>=</prmSeparator>\r
+\r
<parameters>\r
<name>Transition weighting</name>\r
<description>Type of the sequence (PROTEIN or DNA)</description>\r
<max>10</max>\r
</validValue>\r
</parameters>\r
+\r
<parameters>\r
<name>Type</name>\r
<description>Type of the sequence (PROTEIN or DNA)</description>\r
<possibleValues>PROTEIN</possibleValues>\r
<possibleValues>DNA</possibleValues>\r
</parameters>\r
+\r
<parameters>\r
<name>OUTORDER</name>\r
<description>As per INPUT or ALIGNED</description>\r
<possibleValues>INPUT</possibleValues>\r
<possibleValues>ALIGNED</possibleValues>\r
</parameters>\r
+\r
<parameters>\r
<name>MATRIX</name>\r
<description>Protein weight matrix</description>\r
<possibleValues>PAM80</possibleValues>\r
<possibleValues>PAM90</possibleValues>\r
</parameters>\r
+\r
<parameters>\r
<name>GAPOPEN</name>\r
<description>Gap opening penalty</description>\r
<max>1000</max>\r
</validValue>\r
</parameters>\r
+\r
<parameters>\r
<name>-GAPEXT</name>\r
<description>Gap extension penalty</description>\r
<max>10</max>\r
</validValue>\r
</parameters>\r
+\r
<parameters>\r
<name>ENDGAPS</name>\r
<description>End gap separation pen</description>\r
<max>10</max>\r
</validValue>\r
</parameters>\r
+\r
<parameters>\r
<name>GAPDIST</name>\r
<description>Gap separation pen. range</description>\r
<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
<presets>\r
- <runnerClassName>compbio.runner.clustal.ClustalW</runnerClassName>\r
- <preset>\r
- <name>Disable gap weighting (Speed-oriented)</name>\r
- <description></description>\r
- <optlist>\r
- <option>-NOPGAP</option>\r
- <option>-NOWEIGHTS</option>\r
- <option>-NOHGAP</option>\r
- </optlist>\r
- </preset>\r
+ <runnerClassName>compbio.runner.msa.ClustalW</runnerClassName>\r
+ <preset>\r
+ <name>Disable gap weighting (Speed-oriented)</name>\r
+ <description></description>\r
+ <optlist>\r
+ <option>-NOPGAP</option>\r
+ <option>-NOWEIGHTS</option>\r
+ <option>-NOHGAP</option>\r
+ </optlist>\r
+ </preset>\r
</presets>\r
<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
<limits>\r
- <runnerClassName>compbio.runner.clustal.ClustalO</runnerClassName>\r
- <limit isDefault="true">\r
- <seqNumber>2000</seqNumber>\r
- <seqLength>1000</seqLength>\r
- </limit>\r
- <limit isDefault="false">\r
- <preset># LocalEngineExecutionLimit #</preset>\r
- <seqNumber>30</seqNumber>\r
- <seqLength>500</seqLength>\r
- </limit>\r
+ <runnerClassName>compbio.runner.msa.ClustalO</runnerClassName>\r
+ <limit isDefault="true">\r
+ <seqNumber>2000</seqNumber>\r
+ <seqLength>1000</seqLength>\r
+ </limit>\r
+ <limit isDefault="false">\r
+ <preset># LocalEngineExecutionLimit #</preset>\r
+ <seqNumber>30</seqNumber>\r
+ <seqLength>500</seqLength>\r
+ </limit>\r
</limits>\r
<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
<limits>\r
- <runnerClassName>compbio.runner.disorder.Disembl</runnerClassName>\r
- <limit isDefault="true">\r
- <seqNumber>5000</seqNumber>\r
- <seqLength>1000</seqLength>\r
- </limit>\r
- <limit isDefault="false">\r
- <preset># LocalEngineExecutionLimit #</preset>\r
- <seqNumber>200</seqNumber>\r
- <seqLength>400</seqLength>\r
- </limit>\r
+ <runnerClassName>compbio.runner.disorder.Disembl</runnerClassName>\r
+ <limit isDefault="true">\r
+ <seqNumber>5000</seqNumber>\r
+ <seqLength>1000</seqLength>\r
+ </limit>\r
+ <limit isDefault="false">\r
+ <preset># LocalEngineExecutionLimit #</preset>\r
+ <seqNumber>200</seqNumber>\r
+ <seqLength>400</seqLength>\r
+ </limit>\r
</limits>\r
<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
<runnerConfig>\r
-<!-- \r
- Extreme variation of this parameter does not have any impact on the output\r
- so irrelevant. \r
+<!-- Extreme variation of this parameter does not have any impact on the output so irrelevant.\r
+ <runnerClassName>compbio.runner.disorder.Disembl</runnerClassName>\r
+\r
+ <prmSeparator>=</prmSeparator>\r
+\r
+ <parameters>\r
+ <name>Savitzky-Golay smoothing frame</name>\r
+ <description>Algorithm Parameter: Savitzky-Golay smoothing frame</description>\r
+ <optionNames>sg</optionNames>\r
+ <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
+ <defaultValue>8</defaultValue>\r
+ <validValue>\r
+ <type>Integer</type>\r
+ <min>1</min>\r
+ <max>30</max>\r
+ </validValue>\r
+ </parameters>\r
\r
- <runnerClassName>compbio.runner.disorder.Disembl</runnerClassName>\r
- <prmSeparator>=</prmSeparator>\r
- <parameters>\r
- <name>Savitzky-Golay smoothing frame</name>\r
- <description>Algorithm Parameter: Savitzky-Golay smoothing frame</description>\r
- <optionNames>sg</optionNames>\r
- <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
- <defaultValue>8</defaultValue>\r
- <validValue>\r
- <type>Integer</type>\r
- <min>1</min>\r
- <max>30</max>\r
- </validValue>\r
- </parameters>\r
- \r
These can be supported but not recommended to change so what's the point?\r
- \r
Manual: Normally the default parameters should not be changed.\r
\r
- <parameters>\r
- <name>Minimum peak width</name>\r
- <description>Algorithm Parameter: Minimum peak width.</description>\r
- <optionNames>pw</optionNames>\r
- <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
- <defaultValue>8</defaultValue>\r
- <validValue>\r
- <type>Integer</type>\r
- <min>1</min>\r
- <max>30</max>\r
- </validValue>\r
- </parameters>\r
- <parameters>\r
- <name>Maximum join distance</name>\r
- <description>Algorithm Parameter: Maximum join distance</description>\r
- <optionNames>jd</optionNames>\r
- <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
- <defaultValue>4</defaultValue>\r
- <validValue>\r
- <type>Integer</type>\r
- <min>1</min>\r
- <max>30</max>\r
- </validValue>\r
- </parameters>\r
- <parameters>\r
- <name>Coils threshold</name>\r
- <description>Stringency values for different predictor: Coils threshold</description>\r
- <optionNames>ct</optionNames>\r
- <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
- <defaultValue>1.2</defaultValue>\r
- <validValue>\r
- <type>Float</type>\r
- <min>0.1</min>\r
- <max>10</max>\r
- </validValue>\r
- </parameters>\r
- <parameters>\r
- <name>Remark465 threshold</name>\r
- <description>Stringency values for different predictor: Remark465 threshold</description>\r
- <optionNames>rt</optionNames>\r
- <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
- <defaultValue>1.4</defaultValue>\r
- <validValue>\r
- <type>Float</type>\r
- <min>0.1</min>\r
- <max>10</max>\r
- </validValue>\r
- </parameters>\r
- <parameters>\r
- <name>Hot loops threshold</name>\r
- <description>Stringency values for different predictor: Hot loops threshold.</description>\r
- <optionNames>lt</optionNames>\r
- <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
- <defaultValue>1.2</defaultValue>\r
- <validValue>\r
- <type>Float</type>\r
- <min>0.1</min>\r
- <max>10</max>\r
- </validValue>\r
- </parameters>\r
- -->\r
+ <parameters>\r
+ <name>Minimum peak width</name>\r
+ <description>Algorithm Parameter: Minimum peak width.</description>\r
+ <optionNames>pw</optionNames>\r
+ <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
+ <defaultValue>8</defaultValue>\r
+ <validValue>\r
+ <type>Integer</type>\r
+ <min>1</min>\r
+ <max>30</max>\r
+ </validValue>\r
+ </parameters>\r
+\r
+ <parameters>\r
+ <name>Maximum join distance</name>\r
+ <description>Algorithm Parameter: Maximum join distance</description>\r
+ <optionNames>jd</optionNames>\r
+ <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
+ <defaultValue>4</defaultValue>\r
+ <validValue>\r
+ <type>Integer</type>\r
+ <min>1</min>\r
+ <max>30</max>\r
+ </validValue>\r
+ </parameters>\r
+\r
+ <parameters>\r
+ <name>Coils threshold</name>\r
+ <description>Stringency values for different predictor: Coils threshold</description>\r
+ <optionNames>ct</optionNames>\r
+ <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
+ <defaultValue>1.2</defaultValue>\r
+ <validValue>\r
+ <type>Float</type>\r
+ <min>0.1</min>\r
+ <max>10</max>\r
+ </validValue>\r
+ </parameters>\r
+\r
+ <parameters>\r
+ <name>Remark465 threshold</name>\r
+ <description>Stringency values for different predictor: Remark465 threshold</description>\r
+ <optionNames>rt</optionNames>\r
+ <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
+ <defaultValue>1.4</defaultValue>\r
+ <validValue>\r
+ <type>Float</type>\r
+ <min>0.1</min>\r
+ <max>10</max>\r
+ </validValue>\r
+ </parameters>\r
\r
+ <parameters>\r
+ <name>Hot loops threshold</name>\r
+ <description>Stringency values for different predictor: Hot loops threshold.</description>\r
+ <optionNames>lt</optionNames>\r
+ <furtherDetails>prog_docs/disembl.html</furtherDetails>\r
+ <defaultValue>1.2</defaultValue>\r
+ <validValue>\r
+ <type>Float</type>\r
+ <min>0.1</min>\r
+ <max>10</max>\r
+ </validValue>\r
+ </parameters>\r
+-->\r
</runnerConfig>\r
<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
<limits>\r
- <runnerClassName>compbio.runner.disorder.GlobPlot</runnerClassName>\r
- <limit isDefault="true">\r
- <seqNumber>5000</seqNumber>\r
- <seqLength>1000</seqLength>\r
- </limit>\r
- <limit isDefault="false">\r
- <preset># LocalEngineExecutionLimit #</preset>\r
- <seqNumber>200</seqNumber>\r
- <seqLength>400</seqLength>\r
- </limit>\r
+ <runnerClassName>compbio.runner.disorder.GlobPlot</runnerClassName>\r
+ <limit isDefault="true">\r
+ <seqNumber>5000</seqNumber>\r
+ <seqLength>1000</seqLength>\r
+ </limit>\r
+ <limit isDefault="false">\r
+ <preset># LocalEngineExecutionLimit #</preset>\r
+ <seqNumber>200</seqNumber>\r
+ <seqLength>400</seqLength>\r
+ </limit>\r
</limits>\r
<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
<limits>\r
- <runnerClassName>compbio.runner.disorder.IUPred</runnerClassName>\r
- <limit isDefault="true">\r
- <seqNumber>5000</seqNumber>\r
- <seqLength>1000</seqLength>\r
- </limit>\r
- <limit isDefault="false">\r
- <preset># LocalEngineExecutionLimit #</preset>\r
- <seqNumber>50</seqNumber>\r
- <seqLength>400</seqLength>\r
- </limit>\r
+ <runnerClassName>compbio.runner.disorder.IUPred</runnerClassName>\r
+ <limit isDefault="true">\r
+ <seqNumber>5000</seqNumber>\r
+ <seqLength>1000</seqLength>\r
+ </limit>\r
+ <limit isDefault="false">\r
+ <preset># LocalEngineExecutionLimit #</preset>\r
+ <seqNumber>50</seqNumber>\r
+ <seqLength>400</seqLength>\r
+ </limit>\r
</limits>\r
<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
<runnerConfig>\r
- <runnerClassName>compbio.runner.disorder.IUPred</runnerClassName>\r
- <options isRequired="true">\r
+ <runnerClassName>compbio.runner.disorder.IUPred</runnerClassName>\r
+\r
+ <options isRequired="true">\r
<name>Disorder type</name>\r
- <description> "Long" - for prediction of long disordered regions, "short" - for \r
- prediction of short disordered regions ( e.g. missing residues in\r
- X-ray structures) and "glob" for predicting globular domains. "All" for all methods</description>\r
+ <description>\r
+ "Long" - for prediction of long disordered regions, "short" - for \r
+ prediction of short disordered regions ( e.g. missing residues in\r
+ X-ray structures) and "glob" for predicting globular domains.\r
+ "All" for all methods\r
+ </description>\r
<optionNames>short</optionNames>\r
<optionNames>long</optionNames>\r
<optionNames>glob</optionNames>\r
<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
<limits>\r
- <runnerClassName>compbio.runner.disorder.Jronn</runnerClassName>\r
- <limit isDefault="true">\r
- <seqNumber>2000</seqNumber>\r
- <seqLength>2000</seqLength>\r
- </limit>\r
- <limit isDefault="false">\r
- <preset># LocalEngineExecutionLimit #</preset>\r
- <seqNumber>5</seqNumber>\r
- <seqLength>500</seqLength>\r
- </limit>\r
+ <runnerClassName>compbio.runner.disorder.Jronn</runnerClassName>\r
+ <limit isDefault="true">\r
+ <seqNumber>2000</seqNumber>\r
+ <seqLength>2000</seqLength>\r
+ </limit>\r
+ <limit isDefault="false">\r
+ <preset># LocalEngineExecutionLimit #</preset>\r
+ <seqNumber>5</seqNumber>\r
+ <seqLength>500</seqLength>\r
+ </limit>\r
</limits>\r
<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
<limits>\r
- <runnerClassName>compbio.runner.muscle.Muscle</runnerClassName>\r
- <limit isDefault="true">\r
- <seqNumber>1000</seqNumber>\r
- <seqLength>1000</seqLength>\r
- </limit>\r
- <limit isDefault="false">\r
- <preset># LocalEngineExecutionLimit #</preset>\r
- <seqNumber>20</seqNumber>\r
- <seqLength>500</seqLength>\r
- </limit>\r
- \r
- <!-- Separate limits for presets -->\r
- <limit isDefault="false">\r
- <preset>Protein alignment(Fastest speed)</preset>\r
- <seqNumber>2000</seqNumber>\r
- <seqLength>1000</seqLength>\r
- </limit>\r
- <limit isDefault="false">\r
- <preset>Nucleotide alignment(Fastest speed)</preset>\r
- <seqNumber>1000</seqNumber>\r
- <seqLength>3000</seqLength>\r
- </limit>\r
- <limit isDefault="false">\r
- <preset>Huge alignments (speed-oriented)</preset>\r
- <seqNumber>2000</seqNumber>\r
- <seqLength>3000</seqLength>\r
- </limit>\r
- \r
+ <runnerClassName>compbio.runner.msa.Muscle</runnerClassName>\r
+\r
+ <limit isDefault="true">\r
+ <seqNumber>1000</seqNumber>\r
+ <seqLength>1000</seqLength>\r
+ </limit>\r
+\r
+ <limit isDefault="false">\r
+ <preset># LocalEngineExecutionLimit #</preset>\r
+ <seqNumber>20</seqNumber>\r
+ <seqLength>500</seqLength>\r
+ </limit>\r
+\r
+ <!-- Separate limits for presets -->\r
+ <limit isDefault="false">\r
+ <preset>Protein alignment(Fastest speed)</preset>\r
+ <seqNumber>2000</seqNumber>\r
+ <seqLength>1000</seqLength>\r
+ </limit>\r
+\r
+ <limit isDefault="false">\r
+ <preset>Nucleotide alignment(Fastest speed)</preset>\r
+ <seqNumber>1000</seqNumber>\r
+ <seqLength>3000</seqLength>\r
+ </limit>\r
+\r
+ <limit isDefault="false">\r
+ <preset>Huge alignments (speed-oriented)</preset>\r
+ <seqNumber>2000</seqNumber>\r
+ <seqLength>3000</seqLength>\r
+ </limit>\r
</limits>\r
<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
<runnerConfig>\r
- <runnerClassName>compbio.runner.muscle.Muscle</runnerClassName>\r
- <!--\r
+ <runnerClassName>compbio.runner.msa.Muscle</runnerClassName>\r
+\r
+<!--\r
This is the only option possible so no point in having it \r
<options isRequired="false">\r
<name>Group sequences</name>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
<defaultValue>-group</defaultValue>\r
</options>\r
- -->\r
- <!-- optionNames>-stable</optionNames this is commented out as it contain bug see muscle web site-->\r
+-->\r
+\r
+<!-- optionNames>-stable</optionNames this is commented out as it contain bug see muscle web site-->\r
+\r
<options isRequired="false">\r
<name>Anchor optimisation</name>\r
- <description>Enable/disable anchor optimization in tree dependent refinement iterations</description>\r
+ <description>\r
+ Enable/disable anchor optimization in tree dependent refinement iterations\r
+ </description>\r
<optionNames>-anchors</optionNames>\r
<optionNames>-noanchors</optionNames>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
<defaultValue>-anchors</defaultValue>\r
</options>\r
- <!-- Programs failures often with this option \r
+\r
+<!-- Programs failures often with this option \r
<options isRequired="false">\r
<name>Window refine</name>\r
<description>Refine an alignment by dividing it into non-overlapping windows and re-aligning each window. Typically used for whole-genome nucleotide alignments</description>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
<defaultValue>-refinew</defaultValue>\r
</options>\r
- -->\r
+-->\r
+\r
<options isRequired="false">\r
<name>Root alignment computation method</name>\r
- <description>Use Steven Brenner's method for computing the root alignment.</description>\r
+ <description>\r
+ Use Steven Brenner's method for computing the root alignment.\r
+ </description>\r
<optionNames>-brenner</optionNames>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
</options>\r
- <!-- This option make sense only in conjunction with -tree which we do not currently support\r
+\r
+<!-- This option make sense only in conjunction with -tree which we do not currently support\r
<options isRequired="false">\r
<name>Fast clustering of input sequences</name>\r
<description>Perform fast clustering of input sequences.</description>\r
<optionNames>-cluster</optionNames>\r
<furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
</options>\r
- -->\r
- <options isRequired="false">\r
+-->\r
+\r
+ <options isRequired="false">\r
<name>dimer</name>\r
- <description>Use dimer approximation for the SP score (faster, slightly less accurate)</description>\r
+ <description>\r
+ Use dimer approximation for the SP score (faster, slightly less accurate)\r
+ </description>\r
<optionNames>-dimer</optionNames>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
- </options>\r
+ </options>\r
+\r
<options isRequired="false">\r
<name>Diagonal</name>\r
- <description>Use diagonal optimizations. Faster, especially for closely related sequences, but may be less accurate.</description>\r
+ <description>\r
+ Use diagonal optimizations. Faster, especially for closely related sequences, but may be less accurate.\r
+ </description>\r
<optionNames>-diags</optionNames>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
</options>\r
+\r
<options isRequired="false">\r
<name>Diagonal 1</name>\r
- <description>Use diagonal optimizations in first iteration (faster for similar sequences)</description>\r
+ <description>\r
+ Use diagonal optimizations in first iteration (faster for similar sequences)\r
+ </description>\r
<optionNames>-diags1</optionNames>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
</options>\r
- <options isRequired="false">\r
+\r
+ <options isRequired="false">\r
<name>Profile scoring method</name>\r
- <description>le - use log-expectation profile score VTML240 (default for amino acid sequences.)\r
- sp - use sum-of-pairs protein profile score (PAM200).\r
- sv - use sum-of-pairs profile score (VTML240)</description>\r
+ <description>\r
+ le - use log-expectation profile score VTML240 (default for amino acid sequences.)\r
+ sp - use sum-of-pairs protein profile score (PAM200).\r
+ sv - use sum-of-pairs profile score (VTML240)</description>\r
<optionNames>-le</optionNames>\r
<optionNames>-sp</optionNames>\r
<optionNames>-sv</optionNames>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
- <defaultValue>-le</defaultValue>\r
+ <defaultValue>-le</defaultValue>\r
</options>\r
+\r
<prmSeparator> </prmSeparator>\r
- <parameters isRequired="false">\r
+\r
+ <parameters isRequired="false">\r
<name>Sequence type</name>\r
- <description>Sequence type - Amino acid/Nucleotide </description>\r
+ <description>\r
+ Sequence type - Amino acid/Nucleotide\r
+ </description>\r
<optionNames>-seqtype</optionNames>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
<defaultValue>auto</defaultValue>\r
<possibleValues>dna</possibleValues>\r
<possibleValues>rna</possibleValues>\r
</parameters>\r
- <parameters isRequired="false">\r
+\r
+ <parameters isRequired="false">\r
<name>Maxiters</name>\r
- <description>Maximum number of iterations (integer, default 16)</description>\r
+ <description>\r
+ Maximum number of iterations (integer, default 16)\r
+ </description>\r
<optionNames>-maxiters</optionNames>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
<defaultValue>16</defaultValue>\r
<validValue>\r
- <type>Integer</type>\r
+ <type>Integer</type>\r
<min>1</min>\r
<max>100</max>\r
</validValue>\r
</parameters>\r
- <!-- disable as refinew is disabled \r
+\r
+<!-- disable as refinew is disabled \r
<parameters isRequired="false">\r
<name>Maxiters</name>\r
<description>Length of window for Window Refine (-refinew)</description>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
<defaultValue>200</defaultValue>\r
<validValue>\r
- <type>Integer</type>\r
+ <type>Integer</type>\r
<min>1</min>\r
<max>1000</max>\r
</validValue>\r
</parameters>\r
- -->\r
+-->\r
+\r
<parameters isRequired="false">\r
<name>Diagonal break</name>\r
- <description>Maximum distance between two diagonals that allows them to merge into one diagonal</description>\r
+ <description>\r
+ Maximum distance between two diagonals that allows them to merge into one diagonal\r
+ </description>\r
<optionNames>-diagbreak</optionNames>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
<defaultValue>1</defaultValue>\r
<validValue>\r
- <type>Integer</type>\r
+ <type>Integer</type>\r
<min>1</min>\r
<max>100</max>\r
</validValue>\r
</parameters>\r
+\r
<parameters isRequired="false">\r
<name>Diagonal length</name>\r
<description>Minimum length of diagonal</description>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
<defaultValue>24</defaultValue>\r
<validValue>\r
- <type>Integer</type>\r
+ <type>Integer</type>\r
<min>2</min>\r
<max>100</max>\r
</validValue>\r
</parameters>\r
+\r
<parameters isRequired="false">\r
<name>Diagonal margin</name>\r
- <description>Discard this many positions at ends of diagonal</description>\r
+ <description>\r
+ Discard this many positions at ends of diagonal\r
+ </description>\r
<optionNames>-diagmargin</optionNames>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
<defaultValue>5</defaultValue>\r
<validValue>\r
- <type>Integer</type>\r
+ <type>Integer</type>\r
<min>1</min>\r
<max>100</max>\r
</validValue>\r
</parameters>\r
+\r
<parameters isRequired="false">\r
<name>Anchor spacing</name>\r
- <description>Minimum spacing between anchor columns</description>\r
+ <description>\r
+ Minimum spacing between anchor columns\r
+ </description>\r
<optionNames>-anchorspacing</optionNames>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
<defaultValue>32</defaultValue>\r
<validValue>\r
- <type>Integer</type>\r
+ <type>Integer</type>\r
<min>2</min>\r
<max>1000</max>\r
</validValue>\r
</parameters>\r
- <parameters isRequired="false">\r
+\r
+ <parameters isRequired="false">\r
<name>Matrix</name>\r
- <description>Substitution Matrix to use</description>\r
+ <description>\r
+ Substitution Matrix to use\r
+ </description>\r
<optionNames>-matrix</optionNames>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
<defaultValue>BLOSUM62</defaultValue>\r
- <possibleValues>BLOSUM100</possibleValues>\r
- <possibleValues>BLOSUM30</possibleValues>\r
- <possibleValues>BLOSUM35</possibleValues>\r
- <possibleValues>BLOSUM40</possibleValues>\r
- <possibleValues>BLOSUM45</possibleValues>\r
- <possibleValues>BLOSUM50</possibleValues>\r
- <possibleValues>BLOSUM55</possibleValues>\r
- <possibleValues>BLOSUM60</possibleValues>\r
- <possibleValues>BLOSUM62</possibleValues>\r
- <possibleValues>BLOSUM65</possibleValues>\r
- <possibleValues>BLOSUM70</possibleValues>\r
- <possibleValues>BLOSUM75</possibleValues>\r
- <possibleValues>BLOSUM80</possibleValues>\r
- <possibleValues>BLOSUM85</possibleValues>\r
- <possibleValues>BLOSUM90</possibleValues>\r
- <possibleValues>BLOSUMN</possibleValues>\r
- <possibleValues>DAYHOFF</possibleValues>\r
- <possibleValues>GONNET</possibleValues>\r
- <possibleValues>IDENTITY</possibleValues>\r
- <possibleValues>MATCH</possibleValues>\r
- <possibleValues>NUC.4.2</possibleValues>\r
- <possibleValues>NUC.4.4</possibleValues>\r
- <possibleValues>PAM10</possibleValues>\r
- <possibleValues>PAM100</possibleValues>\r
- <possibleValues>PAM110</possibleValues>\r
- <possibleValues>PAM120</possibleValues>\r
- <possibleValues>PAM130</possibleValues>\r
- <possibleValues>PAM140</possibleValues>\r
- <possibleValues>PAM150</possibleValues>\r
- <possibleValues>PAM160</possibleValues>\r
- <possibleValues>PAM170</possibleValues>\r
- <possibleValues>PAM180</possibleValues>\r
- <possibleValues>PAM190</possibleValues>\r
- <possibleValues>PAM20</possibleValues>\r
- <possibleValues>PAM200</possibleValues>\r
- <possibleValues>PAM210</possibleValues>\r
- <possibleValues>PAM220</possibleValues>\r
- <possibleValues>PAM230</possibleValues>\r
- <possibleValues>PAM240</possibleValues>\r
- <possibleValues>PAM250</possibleValues>\r
- <possibleValues>PAM260</possibleValues>\r
- <possibleValues>PAM270</possibleValues>\r
- <possibleValues>PAM280</possibleValues>\r
- <possibleValues>PAM290</possibleValues>\r
- <possibleValues>PAM30</possibleValues>\r
- <possibleValues>PAM300</possibleValues>\r
- <possibleValues>PAM310</possibleValues>\r
- <possibleValues>PAM320</possibleValues>\r
- <possibleValues>PAM330</possibleValues>\r
- <possibleValues>PAM340</possibleValues>\r
- <possibleValues>PAM350</possibleValues>\r
- <possibleValues>PAM360</possibleValues>\r
- <possibleValues>PAM370</possibleValues>\r
- <possibleValues>PAM380</possibleValues>\r
- <possibleValues>PAM390</possibleValues>\r
- <possibleValues>PAM40</possibleValues>\r
- <possibleValues>PAM400</possibleValues>\r
- <possibleValues>PAM410</possibleValues>\r
- <possibleValues>PAM420</possibleValues>\r
- <possibleValues>PAM430</possibleValues>\r
- <possibleValues>PAM440</possibleValues>\r
- <possibleValues>PAM450</possibleValues>\r
- <possibleValues>PAM460</possibleValues>\r
- <possibleValues>PAM470</possibleValues>\r
- <possibleValues>PAM480</possibleValues>\r
- <possibleValues>PAM490</possibleValues>\r
- <possibleValues>PAM50</possibleValues>\r
- <possibleValues>PAM500</possibleValues>\r
- <possibleValues>PAM60</possibleValues>\r
- <possibleValues>PAM70</possibleValues>\r
- <possibleValues>PAM80</possibleValues>\r
- <possibleValues>PAM90</possibleValues>\r
+ <possibleValues>BLOSUM100</possibleValues>\r
+ <possibleValues>BLOSUM30</possibleValues>\r
+ <possibleValues>BLOSUM35</possibleValues>\r
+ <possibleValues>BLOSUM40</possibleValues>\r
+ <possibleValues>BLOSUM45</possibleValues>\r
+ <possibleValues>BLOSUM50</possibleValues>\r
+ <possibleValues>BLOSUM55</possibleValues>\r
+ <possibleValues>BLOSUM60</possibleValues>\r
+ <possibleValues>BLOSUM62</possibleValues>\r
+ <possibleValues>BLOSUM65</possibleValues>\r
+ <possibleValues>BLOSUM70</possibleValues>\r
+ <possibleValues>BLOSUM75</possibleValues>\r
+ <possibleValues>BLOSUM80</possibleValues>\r
+ <possibleValues>BLOSUM85</possibleValues>\r
+ <possibleValues>BLOSUM90</possibleValues>\r
+ <possibleValues>BLOSUMN</possibleValues>\r
+ <possibleValues>DAYHOFF</possibleValues>\r
+ <possibleValues>GONNET</possibleValues>\r
+ <possibleValues>IDENTITY</possibleValues>\r
+ <possibleValues>MATCH</possibleValues>\r
+ <possibleValues>NUC.4.2</possibleValues>\r
+ <possibleValues>NUC.4.4</possibleValues>\r
+ <possibleValues>PAM10</possibleValues>\r
+ <possibleValues>PAM100</possibleValues>\r
+ <possibleValues>PAM110</possibleValues>\r
+ <possibleValues>PAM120</possibleValues>\r
+ <possibleValues>PAM130</possibleValues>\r
+ <possibleValues>PAM140</possibleValues>\r
+ <possibleValues>PAM150</possibleValues>\r
+ <possibleValues>PAM160</possibleValues>\r
+ <possibleValues>PAM170</possibleValues>\r
+ <possibleValues>PAM180</possibleValues>\r
+ <possibleValues>PAM190</possibleValues>\r
+ <possibleValues>PAM20</possibleValues>\r
+ <possibleValues>PAM200</possibleValues>\r
+ <possibleValues>PAM210</possibleValues>\r
+ <possibleValues>PAM220</possibleValues>\r
+ <possibleValues>PAM230</possibleValues>\r
+ <possibleValues>PAM240</possibleValues>\r
+ <possibleValues>PAM250</possibleValues>\r
+ <possibleValues>PAM260</possibleValues>\r
+ <possibleValues>PAM270</possibleValues>\r
+ <possibleValues>PAM280</possibleValues>\r
+ <possibleValues>PAM290</possibleValues>\r
+ <possibleValues>PAM30</possibleValues>\r
+ <possibleValues>PAM300</possibleValues>\r
+ <possibleValues>PAM310</possibleValues>\r
+ <possibleValues>PAM320</possibleValues>\r
+ <possibleValues>PAM330</possibleValues>\r
+ <possibleValues>PAM340</possibleValues>\r
+ <possibleValues>PAM350</possibleValues>\r
+ <possibleValues>PAM360</possibleValues>\r
+ <possibleValues>PAM370</possibleValues>\r
+ <possibleValues>PAM380</possibleValues>\r
+ <possibleValues>PAM390</possibleValues>\r
+ <possibleValues>PAM40</possibleValues>\r
+ <possibleValues>PAM400</possibleValues>\r
+ <possibleValues>PAM410</possibleValues>\r
+ <possibleValues>PAM420</possibleValues>\r
+ <possibleValues>PAM430</possibleValues>\r
+ <possibleValues>PAM440</possibleValues>\r
+ <possibleValues>PAM450</possibleValues>\r
+ <possibleValues>PAM460</possibleValues>\r
+ <possibleValues>PAM470</possibleValues>\r
+ <possibleValues>PAM480</possibleValues>\r
+ <possibleValues>PAM490</possibleValues>\r
+ <possibleValues>PAM50</possibleValues>\r
+ <possibleValues>PAM500</possibleValues>\r
+ <possibleValues>PAM60</possibleValues>\r
+ <possibleValues>PAM70</possibleValues>\r
+ <possibleValues>PAM80</possibleValues>\r
+ <possibleValues>PAM90</possibleValues>\r
</parameters>\r
+\r
<parameters>\r
<name>Gap open penalty</name>\r
- <description>Gap opening penalty. Must be negative</description>\r
+ <description>\r
+ Gap opening penalty. Must be negative\r
+ </description>\r
<optionNames>-gapopen</optionNames>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
<defaultValue>-12.0</defaultValue>\r
<validValue>\r
- <type>Float</type>\r
+ <type>Float</type>\r
<min>-100</min>\r
<max>0</max>\r
</validValue>\r
</parameters>\r
+\r
<parameters>\r
<name>Gap extension penalty</name>\r
- <description>Gap extension penalty. Must be negative</description>\r
+ <description>\r
+ Gap extension penalty. Must be negative\r
+ </description>\r
<optionNames>-gapextend</optionNames>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
<defaultValue>-1.0</defaultValue>\r
<validValue>\r
- <type>Float</type>\r
+ <type>Float</type>\r
<min>-100</min>\r
<max>0</max>\r
</validValue>\r
</parameters>\r
+\r
<parameters>\r
<name>Center</name>\r
- <description>Center parameter. Should be negative.</description>\r
+ <description>\r
+ Center parameter. Should be negative.\r
+ </description>\r
<optionNames>-center</optionNames>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
<defaultValue>0.0</defaultValue>\r
<validValue>\r
- <type>Float</type>\r
+ <type>Float</type>\r
<min>-100</min>\r
<max>0</max>\r
</validValue>\r
</parameters>\r
+\r
<parameters>\r
<name>Hydro</name>\r
- <description>Window size for determining whether a region is hydrophobic.</description>\r
+ <description>\r
+ Window size for determining whether a region is hydrophobic.\r
+ </description>\r
<optionNames>-hydro</optionNames>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
<defaultValue>5</defaultValue>\r
<validValue>\r
- <type>Integer</type>\r
+ <type>Integer</type>\r
<min>0</min>\r
<max>100</max>\r
</validValue>\r
</parameters>\r
+\r
<parameters>\r
<name>Hydrofactor</name>\r
- <description>Multiplier for gap open/close penalties in hydrophobic regions.</description>\r
+ <description>\r
+ Multiplier for gap open/close penalties in hydrophobic regions.\r
+ </description>\r
<optionNames>-hydrofactor</optionNames>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
<defaultValue>1.2</defaultValue>\r
<validValue>\r
- <type>Float</type>\r
+ <type>Float</type>\r
<min>0</min>\r
<max>10</max>\r
</validValue>\r
</parameters>\r
<parameters>\r
<name>Minimum anchor score</name>\r
- <description>Minimum score a column must have to be an anchor (default depends on the profile scoring function!)</description>\r
+ <description>\r
+ Minimum score a column must have to be an anchor\r
+ (default depends on the profile scoring function!)\r
+ </description>\r
<optionNames>-minbestcolscore</optionNames>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
<defaultValue>1.2</defaultValue>\r
<validValue>\r
- <type>Float</type>\r
+ <type>Float</type>\r
<min>0</min>\r
<max>10</max>\r
</validValue>\r
</parameters>\r
+\r
<parameters>\r
<name>Minimum smoothed anchor score</name>\r
- <description>Minimum smoothed score a column must have to be an anchor (default depends on the profile scoring function!)</description>\r
+ <description>\r
+ Minimum smoothed score a column must have to be an anchor\r
+ (default depends on the profile scoring function!)\r
+ </description>\r
<optionNames>-minsmoothscore</optionNames>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
<defaultValue>1.2</defaultValue>\r
<validValue>\r
- <type>Float</type>\r
+ <type>Float</type>\r
<min>0</min>\r
<max>10</max>\r
</validValue>\r
</parameters>\r
- <parameters isRequired="false">\r
+\r
+ <parameters isRequired="false">\r
<name>cluster1</name>\r
- <description>Clustering method to use on the iteration 1</description>\r
+ <description>\r
+ Clustering method to use on the iteration 1\r
+ </description>\r
<optionNames>-cluster1</optionNames>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
<defaultValue>upgma</defaultValue>\r
<possibleValues>upgma</possibleValues>\r
</parameters>\r
- <parameters isRequired="false">\r
+\r
+ <parameters isRequired="false">\r
<name>cluster2</name>\r
- <description>Clustering method to use on the iteration 2 and all subsequent itarations</description>\r
+ <description>\r
+ Clustering method to use on the iteration 2 and all subsequent itarations\r
+ </description>\r
<optionNames>-cluster2</optionNames>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
<defaultValue>upgmb</defaultValue>\r
<possibleValues>upgmb</possibleValues>\r
<possibleValues>neighborjoining</possibleValues>\r
</parameters>\r
+\r
<parameters isRequired="false">\r
<name>Sequence weighting scheme 1</name>\r
- <description>Sequence weighting scheme to use on the iteration 1 and 2 \r
- none=all sequences have equal weight.\r
- henikoff=Henikoff & Henikoff weighting scheme.\r
- henikoffpb=Modified Henikoff scheme as used in PSI-BLAST.\r
- clustalw=CLUSTALW method.\r
- threeway=Gotoh three-way method</description>\r
+ <description>\r
+ Sequence weighting scheme to use on the iteration 1 and 2 \r
+ none=all sequences have equal weight.\r
+ henikoff=Henikoff & Henikoff weighting scheme.\r
+ henikoffpb=Modified Henikoff scheme as used in PSI-BLAST.\r
+ clustalw=CLUSTALW method. threeway=Gotoh three-way method\r
+ </description>\r
<optionNames>-weight1</optionNames>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
<defaultValue>clustalw</defaultValue>\r
<possibleValues>clustalw</possibleValues>\r
<possibleValues>threeway</possibleValues>\r
</parameters>\r
+\r
<parameters isRequired="false">\r
<name>Sequence weighting scheme 2</name>\r
- <description>Sequence weighting scheme to use on the iteration 3 and all subsequent \r
- iterations for tree-dependent refinement.\r
- none=all sequences have equal weight.\r
- henikoff=Henikoff & Henikoff weighting scheme.\r
- henikoffpb=Modified Henikoff scheme as used in PSI-BLAST.\r
- clustalw=CLUSTALW method.\r
- threeway=Gotoh three-way method</description>\r
+ <description>\r
+ Sequence weighting scheme to use on the iteration 3 and all subsequent \r
+ iterations for tree-dependent refinement. \r
+ none=all sequences have equal weight.\r
+ henikoff=Henikoff & Henikoff weighting scheme.\r
+ henikoffpb=Modified Henikoff scheme as used in PSI-BLAST.\r
+ clustalw=CLUSTALW method.\r
+ threeway=Gotoh three-way method\r
+ </description>\r
<optionNames>-weight2</optionNames>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
<defaultValue>clustalw</defaultValue>\r
<possibleValues>clustalw</possibleValues>\r
<possibleValues>threeway</possibleValues>\r
</parameters>\r
- <parameters isRequired="false">\r
+\r
+ <parameters isRequired="false">\r
<name>Distance1</name>\r
- <description>Distance measure for iteration 1. Defaults Kmer6_6 (for amino ) or Kmer4_6 (for nucleo)</description>\r
+ <description>\r
+ Distance measure for iteration 1. Defaults Kmer6_6 (for amino ) or Kmer4_6 (for nucleo)\r
+ </description>\r
<optionNames>-distance1</optionNames>\r
<furtherDetails>prog_docs/muscle.html</furtherDetails>\r
<defaultValue>kmer6_6</defaultValue>\r
<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
<presets>\r
- <runnerClassName>compbio.runner.muscle.Muscle</runnerClassName>\r
- <preset>\r
- <name>Protein alignment(Fastest speed)</name>\r
- <description>Fastest possible speed for protein sequences. Gives acceptable quality alignments for closely related sequences</description>\r
- <optlist>\r
- <option>-maxiters 1</option>\r
- <option>-diags</option>\r
- <option>-sv</option>\r
- <option>-distance1 kbit20_3</option>\r
- </optlist>\r
- </preset>\r
- <preset>\r
- <name>Nucleotide alignment(Fastest speed)</name>\r
- <description>Fastest possible speed for nucleotide sequences. Gives acceptable quality alignments for closely related sequences</description>\r
- <optlist>\r
- <option>-maxiters 1</option>\r
- <option>-diags</option>\r
- </optlist>\r
- </preset>\r
- <preset>\r
- <name>Large alignments (balanced)</name>\r
- <description>A large number of sequences (a few thousand), or very long sequences, \r
- then the default settings of may be too slow for practical use. \r
- A good compromise between speed and accuracy is to run just the first two iterations of \r
- the algorithm</description>\r
- <optlist>\r
- <option>-maxiters 2</option>\r
- </optlist>\r
- </preset>\r
+ <runnerClassName>compbio.runner.msa.Muscle</runnerClassName>\r
+\r
+ <preset>\r
+ <name>Protein alignment(Fastest speed)</name>\r
+ <description>\r
+ Fastest possible speed for protein sequences. Gives acceptable quality \r
+ alignments for closely related sequences\r
+ </description>\r
+ <optlist>\r
+ <option>-maxiters 1</option>\r
+ <option>-diags</option>\r
+ <option>-sv</option>\r
+ <option>-distance1 kbit20_3</option>\r
+ </optlist>\r
+ </preset>\r
+\r
+ <preset>\r
+ <name>Nucleotide alignment(Fastest speed)</name>\r
+ <description>\r
+ Fastest possible speed for nucleotide sequences. Gives acceptable quality \r
+ alignments for closely related sequences\r
+ </description>\r
+ <optlist>\r
+ <option>-maxiters 1</option>\r
+ <option>-diags</option>\r
+ </optlist>\r
+ </preset>\r
+\r
+ <preset>\r
+ <name>Large alignments (balanced)</name>\r
+ <description>\r
+ A large number of sequences (a few thousand), or very long sequences, then the default \r
+ settings of may be too slow for practical use. A good compromise between speed and \r
+ accuracy is to run just the first two iterations of the algorithm.\r
+ </description>\r
+ <optlist>\r
+ <option>-maxiters 2</option>\r
+ </optlist>\r
+ </preset>\r
</presets>\r
<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
<limits>\r
- <runnerClassName>compbio.runner.probcons.Probcons</runnerClassName>\r
- <limit isDefault="true">\r
- <seqNumber>1000</seqNumber>\r
- <seqLength>1000</seqLength>\r
- </limit>\r
- <limit isDefault="false">\r
- <preset># LocalEngineExecutionLimit #</preset>\r
- <seqNumber>20</seqNumber>\r
- <seqLength>500</seqLength>\r
- </limit>\r
+ <runnerClassName>compbio.runner.msa.Probcons</runnerClassName>\r
+\r
+ <limit isDefault="true">\r
+ <seqNumber>1000</seqNumber>\r
+ <seqLength>1000</seqLength>\r
+ </limit>\r
+\r
+ <limit isDefault="false">\r
+ <preset># LocalEngineExecutionLimit #</preset>\r
+ <seqNumber>20</seqNumber>\r
+ <seqLength>500</seqLength>\r
+ </limit>\r
</limits>\r
<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
<runnerConfig>\r
- <runnerClassName>compbio.runner.probcons.Probcons</runnerClassName>\r
+ <runnerClassName>compbio.runner.msa.Probcons</runnerClassName>\r
+\r
<!-- This is requires training -t, but training output probabil file instead of the alignment \r
<options>\r
<name>Reestimate EP</name>\r
<furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
</options>\r
-->\r
+\r
<options>\r
<name>Output aligned</name>\r
- <description>Output sequences in alignment order rather than input order</description>\r
+ <description>\r
+ Output sequences in alignment order rather than input order\r
+ </description>\r
<optionNames>-a</optionNames>\r
<furtherDetails>prog_docs/probcons.pdf</furtherDetails>\r
</options>\r
+\r
<prmSeparator> </prmSeparator>\r
- <!-- unsupported in practice \r
+\r
+<!-- unsupported in practice \r
<parameters>\r
<name>MATRIX</name>\r
<description>Protein weight matrix. Specifies the emission probabilities that are to be used for scoring alignments.</description>\r
<possibleValues>PAM80</possibleValues>\r
<possibleValues>PAM90</possibleValues>\r
</parameters>\r
- -->\r
+-->\r
+\r
<parameters>\r
<name>Rounds of pre-training before aligning the sequences</name>\r
- <description>This specifies the number of rounds of EM to be applied on the set of sequences being\r
-aligned. This option is used in case the default parameters are not appropriate for the\r
-particular sequences being aligned; in general, this option is not recommended as it may\r
-lead to unstable alignment parameters.</description>\r
+ <description>\r
+ This specifies the number of rounds of EM to be applied on the set of sequences being\r
+ aligned. This option is used in case the default parameters are not appropriate for the\r
+ particular sequences being aligned; in general, this option is not recommended as it may\r
+ lead to unstable alignment parameters.\r
+ </description>\r
<optionNames>-pre</optionNames>\r
<furtherDetails>prog_docs/probcons.pdf</furtherDetails>\r
<defaultValue>0</defaultValue>\r
<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
<limits>\r
- <runnerClassName>compbio.runner.tcoffee.Tcoffee</runnerClassName>\r
- <limit isDefault="true">\r
- <seqNumber>1000</seqNumber>\r
- <seqLength>1000</seqLength>\r
- </limit>\r
- <limit isDefault="false">\r
- <preset># LocalEngineExecutionLimit #</preset>\r
- <seqNumber>15</seqNumber>\r
- <seqLength>400</seqLength>\r
- </limit>\r
+ <runnerClassName>compbio.runner.msa.Tcoffee</runnerClassName>\r
\r
- <!-- Limits for presets -->\r
- <limit isDefault="false">\r
- <preset>Quick align. Very fast approximate (Speed-oriented)</preset>\r
- <seqNumber>1000</seqNumber>\r
- <seqLength>3000</seqLength>\r
- </limit>\r
+ <limit isDefault="true">\r
+ <seqNumber>1000</seqNumber>\r
+ <seqLength>1000</seqLength>\r
+ </limit>\r
+ <limit isDefault="false">\r
+ <preset># LocalEngineExecutionLimit #</preset>\r
+ <seqNumber>15</seqNumber>\r
+ <seqLength>400</seqLength>\r
+ </limit>\r
+\r
+ <!-- Limits for presets -->\r
+ <limit isDefault="false">\r
+ <preset>Quick align. Very fast approximate (Speed-oriented)</preset>\r
+ <seqNumber>1000</seqNumber>\r
+ <seqLength>3000</seqLength>\r
+ </limit>\r
\r
</limits>\r
<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
<runnerConfig>\r
- <runnerClassName>compbio.runner.tcoffee.Tcoffee</runnerClassName>\r
+ <runnerClassName>compbio.runner.msa.Tcoffee</runnerClassName>\r
\r
<options isRequired="false">\r
<name>Search sequences in PDB</name>\r
<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
<presets>\r
- <runnerClassName>compbio.runner.tcoffee.Tcoffee</runnerClassName>\r
+ <runnerClassName>compbio.runner.msa.Tcoffee</runnerClassName>\r
+\r
<preset>\r
<name>Quick align. Very fast approximate (Speed-oriented)</name>\r
<description>quickaln: Very fast, sequence type - all, accuracy - medium low</description>\r
<option>-mode quickaln</option>\r
</optlist>\r
</preset>\r
+\r
<!-- does not work\r
<preset>\r
<name>Dali (Speed-oriented)</name>\r
</optlist>\r
</preset>\r
-->\r
+\r
<!-- This requires Blast to operate, however i do not know how to plug it to t-coffee. \r
The build in one does not work. \r
<preset>\r
<option>-mode 3dcoffee</option>\r
</optlist>\r
</preset>\r
+\r
<preset>\r
<name>Accurate (Accuracy-oriented)</name>\r
<description>accurate: slow, sequence type - protein, accuracy - high</description>\r
<option>-mode accurate</option>\r
</optlist>\r
</preset>\r
+\r
could not find templates(?)\r
<preset>\r
<name>Rcoffee for RNA only (accuracy-oriented)</name>\r
</optlist>\r
</preset>\r
-->\r
- <!-- This needs blast\r
+\r
+ <!-- This needs blast\r
<preset>\r
<name>Expresso (accuracy-oriented)</name>\r
<description> expresso: slow, sequence type - all, accuracy - high</description>\r
</optlist>\r
</preset>\r
-->\r
+\r
</presets>\r
git://source.jalview.org / jabaws.git / commitdiff