1 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
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3 <runnerClassName>compbio.runner.muscle.Muscle</runnerClassName>
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4 <options isRequired="false">
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5 <name>Group sequences</name>
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6 <description>Group sequences by similarity (this is the default) or preserve the input order</description>
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7 <optionNames>-group</optionNames>
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8 <optionNames>-stable</optionNames>
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9 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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10 <defaultValue>-stable</defaultValue>
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12 <options isRequired="false">
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13 <name>Anchor optimisation</name>
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14 <description>Enable/disable anchor optimization in tree dependent refinement iterations</description>
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15 <optionNames>-anchors</optionNames>
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16 <optionNames>-noanchors</optionNames>
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17 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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18 <defaultValue>-anchors</defaultValue>
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20 <options isRequired="false">
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21 <name>Root alignment computation method</name>
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22 <description>Use Steven Brenner's method for computing the root alignment.</description>
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23 <optionNames>-brenner</optionNames>
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24 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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26 <!-- This option make sense only in conjunction with -tree which we do not currently support
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27 <options isRequired="false">
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28 <name>Fast clustering of input sequences</name>
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29 <description>Perform fast clustering of input sequences.</description>
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30 <optionNames>-cluster</optionNames>
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31 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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34 <options isRequired="false">
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36 <description>Use dimer approximation for the SP score (faster, slightly less accurate)</description>
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37 <optionNames>-dimer</optionNames>
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38 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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40 <options isRequired="false">
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41 <name>Diagonal</name>
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42 <description>Use diagonal optimizations. Faster, especially for closely related sequences, but may be less accurate.</description>
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43 <optionNames>-diags</optionNames>
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45 <options isRequired="false">
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46 <name>Diagonal 1</name>
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47 <description>Use diagonal optimizations in first iteration (faster for similar sequences)</description>
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48 <optionNames>-diags1</optionNames>
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50 <options isRequired="false">
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51 <name>Profile scoring method</name>
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52 <description>le - use log-expectation profile score VTML240 (default for amino acid sequences.)
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53 sp - use sum-of-pairs protein profile score (PAM200).
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54 sv - use sum-of-pairs profile score (VTML240)</description>
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55 <optionNames>-le</optionNames>
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56 <optionNames>-sp</optionNames>
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57 <optionNames>-sv</optionNames>
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58 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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59 <defaultValue>-le</defaultValue>
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61 <prmSeparator> </prmSeparator>
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62 <parameters isRequired="false">
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63 <name>Sequence type</name>
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64 <description>Sequence type - Amino acid/Nucleotide </description>
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65 <optionNames>-seqtype</optionNames>
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66 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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67 <defaultValue>auto</defaultValue>
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68 <possibleValues>auto</possibleValues>
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69 <possibleValues>protein</possibleValues>
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70 <possibleValues>nucleo</possibleValues>
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72 <parameters isRequired="false">
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73 <name>Maxiters</name>
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74 <description>Maximum number of iterations (integer, default 16)</description>
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75 <optionNames>-maxiters</optionNames>
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76 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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77 <defaultValue>16</defaultValue>
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79 <type>Integer</type>
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85 <parameters isRequired="false">
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87 <description>Substitution Matrix to use</description>
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88 <optionNames>-matrix</optionNames>
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89 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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90 <defaultValue>blosum62</defaultValue>
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91 <possibleValues>blosum62</possibleValues>
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92 <possibleValues>pam250</possibleValues>
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93 <possibleValues>pam100</possibleValues>
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97 <name>Gap open penalty</name>
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98 <description>Gap opening penalty. Must be negative</description>
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99 <optionNames>-gapopen</optionNames>
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100 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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101 <defaultValue>-12.0</defaultValue>
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109 <name>Gap extension penalty</name>
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110 <description>Gap extension penalty. Must be negative</description>
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111 <optionNames>-gapextend</optionNames>
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112 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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113 <defaultValue>-1.0</defaultValue>
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121 <name>Center</name>
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122 <description>Center parameter. Should be negative.</description>
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123 <optionNames>-center</optionNames>
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124 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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125 <defaultValue>0.0</defaultValue>
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134 <description>Window size for determining whether a region is hydrophobic.</description>
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135 <optionNames>-hydro</optionNames>
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136 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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137 <defaultValue>5</defaultValue>
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139 <type>Integer</type>
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145 <name>Hydrofactor</name>
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146 <description>Multiplier for gap open/close penalties in hydrophobic regions.</description>
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147 <optionNames>-hydrofactor</optionNames>
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148 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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149 <defaultValue>1.2</defaultValue>
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156 <parameters isRequired="false">
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157 <name>cluster1</name>
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158 <description>Clustering method to use on the iteration 1</description>
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159 <optionNames>-cluster1</optionNames>
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160 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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161 <defaultValue>upgma</defaultValue>
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162 <possibleValues>upgma</possibleValues>
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164 <parameters isRequired="false">
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165 <name>cluster2</name>
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166 <description>Clustering method to use on the iteration 2 and all subsequent itarations</description>
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167 <optionNames>-cluster2</optionNames>
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168 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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169 <defaultValue>upgmb</defaultValue>
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170 <possibleValues>upgmb</possibleValues>
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171 <possibleValues>neighborjoining</possibleValues>
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173 <parameters isRequired="false">
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174 <name>Sequence weighting scheme 1</name>
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175 <description>Sequence weighting scheme to use on the iteration 1 and 2
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176 none=all sequences have equal weight.
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177 henikoff=Henikoff & Henikoff weighting scheme.
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178 henikoffpb=Modified Henikoff scheme as used in PSI-BLAST.
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179 clustalw=CLUSTALW method.
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180 threeway=Gotoh three-way method</description>
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181 <optionNames>-weight1</optionNames>
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182 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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183 <defaultValue>clustalw</defaultValue>
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184 <possibleValues>none</possibleValues>
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185 <possibleValues>henikoff</possibleValues>
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186 <possibleValues>henikoffpb</possibleValues>
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187 <possibleValues>gsc</possibleValues>
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188 <possibleValues>clustalw</possibleValues>
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189 <possibleValues>threeway</possibleValues>
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191 <parameters isRequired="false">
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192 <name>Sequence weighting scheme 2</name>
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193 <description>Sequence weighting scheme to use on the iteration 3 and all subsequent
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194 iterations for tree-dependent refinement.
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195 none=all sequences have equal weight.
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196 henikoff=Henikoff & Henikoff weighting scheme.
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197 henikoffpb=Modified Henikoff scheme as used in PSI-BLAST.
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198 clustalw=CLUSTALW method.
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199 threeway=Gotoh three-way method</description>
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200 <optionNames>-weight2</optionNames>
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201 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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202 <defaultValue>clustalw</defaultValue>
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203 <possibleValues>none</possibleValues>
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204 <possibleValues>henikoff</possibleValues>
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205 <possibleValues>henikoffpb</possibleValues>
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206 <possibleValues>gsc</possibleValues>
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207 <possibleValues>clustalw</possibleValues>
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208 <possibleValues>threeway</possibleValues>
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210 <parameters isRequired="false">
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211 <name>Distance1</name>
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212 <description>Distance measure for iteration 1. Defaults Kmer6_6 (for amino ) or Kmer4_6 (for nucleo)</description>
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213 <optionNames>-distance1</optionNames>
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214 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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215 <defaultValue>kmer6_6</defaultValue>
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216 <possibleValues>kmer6_6</possibleValues>
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217 <possibleValues>kmer20_3</possibleValues>
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218 <possibleValues>kbit20_3</possibleValues>
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219 <possibleValues>kmer20_4</possibleValues>
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220 <possibleValues>kmer4_6</possibleValues>
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