/var/lib/mobyle/programs/quicktree.xml is in mobyle-programs 5.1.2-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 | <?xml version='1.0' encoding='UTF-8'?>
<!-- XML Authors: Corinne Maufrais, Nicolas Joly and Bertrand Neron, -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>quicktree</name>
<version>1.1</version>
<doc>
<title>QuickTree</title>
<description>
<text lang="en">Rapid reconstruction of phylogenies by the Neighbor-Joining method</text>
</description>
<authors>Kevin Howe, Alex Bateman, Richard Durbin</authors>
<reference>Kevin Howe, Alex Bateman and Richard Durbin (2002).
QuickTree: building huge Neighbour-Joining trees of protein
sequences. Bioinformatics 18(11):1546-1547.</reference>
<comment>
<text lang="en">QuickTree is an efficient implementation of
the Neighbor-Joining algorithm, capable of reconstructing
phylogenies from huge alignments in time less than the age of
the universe.</text>
</comment>
<homepagelink>http://www.sanger.ac.uk/Software/analysis/quicktree/</homepagelink>
<sourcelink>http://www.sanger.ac.uk/Software/analysis/quicktree/</sourcelink>
</doc>
<category>phylogeny:distance</category>
<command>quicktree</command>
</head>
<parameters>
<paragraph>
<name>inpufile</name>
<prompt lang="en">Input file</prompt>
<comment>
<text lang="en">You must enter either a distance matrix or a alignment.</text>
</comment>
<parameters>
<parameter ismandatory="1">
<name>aligfile</name>
<prompt lang="en">Alignment file (-in a)</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>STOCKHOLM</dataFormat>
</type>
<precond>
<code proglang="perl">not defined $distfile or (defined $aligfile and defined $distfile)</code>
<code proglang="python">distfile is None or (distfile and aligfile)</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " -in a $value" : ""</code>
<code proglang="python">( "" , " -in a " + str(value) )[ value is not None ]</code>
</format>
<ctrl>
<message>
<text lang="en">You must enter either a distance matrix or a alignment.</text>
</message>
<code proglang="perl">not $distfile</code>
<code proglang="python">distfile is None</code>
</ctrl>
<argpos>10</argpos>
</parameter>
<parameter ismandatory="1">
<name>distfile</name>
<prompt lang="en">or Distance matrix (-in m)</prompt>
<type>
<datatype>
<class>PhylipDistanceMatrix</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">not defined $aligfile</code>
<code proglang="python">aligfile is None</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " -in m $value" : ""</code>
<code proglang="python">( "" , " -in m " + str(value) )[ value is not None ]</code>
</format>
<ctrl>
<message>
<text lang="en">You must enter either a distance matrix or a alignment.</text>
</message>
<code proglang="perl">not defined $aligfile</code>
<code proglang="python">aligfile is None</code>
</ctrl>
<argpos>10</argpos>
<comment>
<text lang="en">Give a file containing a distance matrix
obtained by distance matrix programs like prodist or
dnadist, ...</text>
</comment>
<example>
5
Alpha 0.000000 0.330447 0.625670 1.032032 1.354086
Beta 0.330447 0.000000 0.375578 1.096290 0.677616
Gamma 0.625670 0.375578 0.000000 0.975798 0.861634
Delta 1.032032 1.096290 0.975798 0.000000 0.226703
Epsilon 1.354086 0.677616 0.861634 0.226703 0.000000
</example>
</parameter>
</parameters>
</paragraph>
<parameter>
<name>out</name>
<prompt lang="en">Output (-out)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>t</value>
</vdef>
<vlist>
<velem>
<value>m</value>
<label>Distance matrix in Phylip format(m)</label>
</velem>
<velem>
<value>t</value>
<label>Tree in New Hampshire format (t)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -out $value" : ""</code>
<code proglang="python">( "" , " -out " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>3</argpos>
</parameter>
<paragraph>
<name>treeopt</name>
<prompt lang="en">Tree output options</prompt>
<precond>
<code proglang="perl">$out ne "m"</code>
<code proglang="python">out != "m"</code>
</precond>
<parameters>
<parameter>
<name>upgma</name>
<prompt lang="en">Use the UPGMA method to construct the tree (-upgma)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -upgma" : ""</code>
<code proglang="python">( "" , " -upgma" )[ value ]</code>
</format>
<argpos>3</argpos>
<comment>
<text lang="en">Bootstrapping is not available for a matrix output</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>aligopt</name>
<prompt lang="en">Alignment options</prompt>
<parameters>
<parameter>
<name>boot</name>
<prompt lang="en">Calculate bootstrap values with n iterations (-boot)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">not defined $distfile and $out ne "m"</code>
<code proglang="python">distfile is None and out != "m"</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " -boot $value" : ""</code>
<code proglang="python">( "" , " -boot " + str(value))[ value is not None ]</code>
</format>
<argpos>3</argpos>
<comment>
<text lang="en">Bootstrapping is not available for a matrix output</text>
</comment>
</parameter>
<parameter>
<name>kimura</name>
<prompt lang="en">Use the kimura translation for pairwise distances (-kimura)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">defined $aligfile</code>
<code proglang="python">aligfile is not None</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -kimura" : ""</code>
<code proglang="python">( "" , " -kimura" )[ value ]</code>
</format>
<argpos>3</argpos>
</parameter>
</parameters>
</paragraph>
<parameter isstdout="1">
<name>treefile</name>
<prompt>Tree file</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<precond>
<code proglang="perl">$out ne "m"</code>
<code proglang="python">out != "m"</code>
</precond>
<filenames>
<code proglang="perl">"quicktree.out"</code>
<code proglang="python">"quicktree.out"</code>
</filenames>
</parameter>
<parameter isstdout="1">
<name>distoutfile</name>
<prompt>Distance matrix</prompt>
<type>
<datatype>
<class>PhylipDistanceMatrix</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$out eq "m"</code>
<code proglang="python">out == "m"</code>
</precond>
<filenames>
<code proglang="perl">"quicktree.out"</code>
<code proglang="python">"quicktree.out"</code>
</filenames>
</parameter>
</parameters>
</program>
|