Mercurial > repos > iuc > hmmer_hmmemit

annotate hmmemit.xml @ 7:96b127c59e6a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 0bccf5220ed6549db7e053f85bbe917326b0a0be"
author iuc
date Wed, 21 Jul 2021 14:11:49 +0000
parents 9415f29a3926
children e9d622609fb5
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f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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1 <?xml version="1.0"?>
3
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2 <tool id="hmmer_hmmemit" name="hmmemit" version="@TOOL_VERSION@">
0
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3 <description>sample sequence(s) from a profile HMM</description>
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4 <macros>
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5 <import>macros.xml</import>
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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6 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <command><![CDATA[
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10 hmmemit
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11
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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12 #if $oformat.oformat_select == "fasta":
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13 -N $oformat.N_fa
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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14 #elif $oformat.oformat_select == "aln":
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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15 -N $oformat.N_aln
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16 -a
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17 #elif $oformat.oformat_select == "mrcs":
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18 -c
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19 #elif $oformat.oformat_select == "mrcsf":
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20 --minl $oformat.minl
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21 --minu $oformat.minu
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22 -C
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23 #else:
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24 -N $oformat.N_smp
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25 -p
3
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26 #if str($oformat.L):
0
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27 -L $oformat.L
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28 #end if
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29 $oformat.emission_profiles
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30 #end if
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31
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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32 @SEED@
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33
3
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34 '$hmmfile'
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35 > '$output'
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36 ]]></command>
0
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37 <inputs>
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38 <expand macro="input_hmm" />
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39
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40 <conditional name="oformat">
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41 <param name="oformat_select" type="select" label="Output Format">
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42 <option value="fasta" selected="true">Fasta</option>
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43 <option value="aln">Alignment</option>
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44 <option value="mrcs">Majority-Rule Concensus Sequence</option>
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45 <option value="mrcsf">Fancier Concensus Sequence</option>
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46 <option value="sample">Sample sequences from profile, not core model</option>
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47 </param>
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48 <when value="fasta">
3
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49 <param name="N_fa" argument="-N" type="integer" min="1" value="1"
0
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50 label="Number of sequences to generate"/>
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51 </when>
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52 <when value="aln">
3
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53 <param name="N_aln" argument="-N" type="integer" min="1" value="1"
0
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54 label="Number of sequences to generate"/>
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55 </when>
3
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56 <when value="mrcs" />
0
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57 <when value="mrcsf">
3
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58 <param argument="--minl" type="float" value="0.7"
0
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59 label="show consensus as 'any' (X/N) unless >= this fraction"/>
3
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60 <param argument="--minu" type="float" value="0.2"
0
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61 label="show consensus as upper case if >= this fraction"/>
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62 </when>
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63 <when value="sample">
3
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64 <param name="N_smp" argument="-N" type="integer" min="1" value="1"
0
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65 label="Number of sequences to generate"/>
3
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66 <param argument="-L" type="integer" optional="true"
0
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67 label="Expected length of profile"/>
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68
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69 <param name="emission_profiles" type="select" label="Emission profile options">
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70 <option value="--local" selected="true">configure profile in multihit local mode</option>
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71 <option value="--unilocal">configure profile in unilocal mode</option>
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72 <option value="--glocal">configure profile in multihit glocal mode</option>
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73 <option value="--uniglocal">configure profile in unihit glocal mode</option>
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74 </param>
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75 </when>
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76 </conditional>
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77
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78 <expand macro="seed"/>
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79 </inputs>
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80 <outputs>
3
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81 <data name="output" format="fasta" label="Sequences generated from $hmmfile.name">
0
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82 <change_format>
5
9415f29a3926 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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83 <when input="oformat.oformat_select" value="aln" format="stockholm"/>
0
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84 <!-- the rest are fasta -->
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85 </change_format>
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86 </data>
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87 </outputs>
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88 <tests>
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89 <test>
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90 <param name="hmmfile" value="globins4.hmm"/>
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91 <param name="oformat_select" value="aln"/>
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92 <param name="N_aln" value="10"/>
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93 <expand macro="seed_test" />
5
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94 <output name="output" file="globins4-emit.sto" ftype="stockholm" compare="sim_size">
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95 <assert_contents>
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96 <has_line_matching expression="# STOCKHOLM.*"/>
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97 <has_line_matching expression="//"/>
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98 </assert_contents>
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99 </output>
0
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100 </test>
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101 <test>
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102 <param name="hmmfile" value="globins4.hmm"/>
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103 <param name="oformat_select" value="fasta"/>
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104 <param name="N_aln" value="10"/>
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105 <expand macro="seed_test" />
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106 <output name="output" file="globins4-emit-1.sto" ftype="fasta" compare="sim_size">
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107 <assert_contents>
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108 <has_line_matching expression=">.*"/>
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109 </assert_contents>
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110 </output>
0
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111 </test>
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112 </tests>
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113 <help><![CDATA[
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114 @HELP_PRE@
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115
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116 The hmmemit program samples (emits) sequences from the profile HMM(s) in
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117 hmmfile, and writes them to output. Sampling sequences may be useful for a
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118 variety of purposes, including creating synthetic true positives for benchmarks
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119 or tests.
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120
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121 The default is to sample one unaligned sequence from the core probability
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122 model, which means that each sequence consists of one full-length domain.
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123 Alternatively, with the -c option, you can emit a simple majority-rule
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124 consensus sequence; or with the -a option, you can emit an alignment (in which
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125 case, you probably also want to set -N to something other than its default of 1
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126 sequence per model).
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127
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128 As another option, with the -p option you can sample a sequence from a fully
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129 configured HMMER search profile. This means sampling a ‘homologous sequence’ by
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130 HMMER’s definition, including nonhomologous flanking sequences, local
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131 alignments, and multiple domains per sequence, depending on the length model
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132 and alignment mode chosen for the profile.
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133
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134 The hmmfile may contain a library of HMMs, in which case each HMM will be used
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135 in turn.
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136
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137 @HELP_PRE_OTH@
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138
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139 Output Formats
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140 --------------
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141
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142 Several output formats are available, each with different options.
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143
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144 **Fasta**
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145
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146 Fasta option is the easiest to understand, given an input model, it will produce N sequences in fasta format from that model.
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147
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148 **Alignment**
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149
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150 Produces a stockholm alignment, of what the Fasta output would have produced.
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151
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152 **Majority-Rule Concensus Sequence**
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153
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154 Emit a plurality-rule consensus sequence, instead of sampling a sequence from
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155 the profile HMM’s probability distribution. The consensus sequence is formed by
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156 selecting the maximum probability residue at each match state.
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157
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158 **Fancier Concensus Sequence**
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159
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160 Emit a fancier plurality-rule consensus sequence than the -c option. If the
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161 maximum probability residue has p < minl show it as a lower case ’any’ residue
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162 (n or x); if p >= minl and < minu show it as a lower case residue; and if p >=
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163 minu show it as an upper case residue. The default settings of minu and minl
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164 are both 0.0, which means -C gives the same output as -c unless you also set
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165 minu and minl to what you want.
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166
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167 **Sample**
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168
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169 Sample unaligned sequences from the implicit search profile, not from the core
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170 model. The core model consists only of the homologous states (between the begin
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171 and end states of a HMMER Plan7 model). The profile includes the nonhomologous
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172 N, C, and J states, local/glocal and uni/multihit algorithm configuration, and
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173 the target length model. Therefore sequences sampled from a profile may in-
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174 clude nonhomologous as well as homologous sequences, and may contain more than
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175 one homologous sequence segment. By default, the profile is in multihit local
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176 mode, and the target sequence length is configured for L=400.
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177
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178 @ATTRIBUTION@
3
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179 ]]></help>
0
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180 <expand macro="citation"/>
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181 </tool>