File: protdist.xml

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<?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>protdist</name>
    <xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/phylip_package.xml"/>
    <doc>
      <title>protdist</title>
      <description>
        <text lang="en">Compute distance matrix from protein sequences</text>
      </description>
      <doclink>http://bioweb2.pasteur.fr/docs/phylip/doc/protdist.html</doclink>
      <comment>
        <text lang="en">This program uses protein sequences to compute
	  a distance matrix, under four different models of amino acid
	  replacement. It can also compute a table of similarity between
	  the amino acid sequences.</text>
        <text lang="en">The distance for each pair of species estimates the
	  total branch length between the two species, and can be used in the
	  distance matrix programs FITCH, KITSCH or NEIGHBOR.</text>
      </comment>
    </doc>
    <category>phylogeny:distance</category>
  </head>
  <parameters>
    <parameter iscommand="1" ishidden="1">
      <name>protdist</name>
      <type>
        <datatype>
          <class>String</class>
        </datatype>
      </type>
      <format>
        <code proglang="perl">"protdist &lt;protdist.params"</code>
        <code proglang="python">"protdist &lt;protdist.params"</code>
      </format>
      <argpos>0</argpos>
    </parameter>
    <parameter ismandatory="1" issimple="1" ismaininput="1">
      <name>infile</name>
      <prompt lang="en">Alignment File</prompt>
      <type>
        <biotype>Protein</biotype>
        <datatype>
          <class>Alignment</class>
        </datatype>
        <dataFormat>PHYLIPI</dataFormat>
      </type>
      <format>
        <code proglang="perl">"ln -s $infile infile &amp;&amp; "</code>
        <code proglang="python">"ln -s " + str( infile ) + " infile &amp;&amp; "</code>
      </format>
      <ctrl>
        <message>
          <text lang="en">the name of this data can't be "infile" or "outfile"</text>
        </message>
        <code proglang="perl">$value ne "infile" and $value ne "outfile"</code>
        <code proglang="python">value not in ( "infile" , "outfile" )</code>
      </ctrl>
      <argpos>-10</argpos>
      <comment>
        <text lang="en">The input file must contained aligned sequences in PHYLIP format obtained by sequence alignment programs.</text>
      </comment>
      <example>
   5   13
Alpha     AACGTGGCCACAT
Beta      AAGGTCGCCACAC
Gamma     CAGTTCGCCACAA
Delta     GAGATTTCCGCCT
Epsilon   GAGATCTCCGCCC
      </example>
    </parameter>
    <parameter>
      <name>Method</name>
      <prompt lang="en">Distance model (P)</prompt>
      <type>
        <datatype>
          <class>Choice</class>
        </datatype>
      </type>
      <vdef>
        <value>J</value>
      </vdef>
      <flist>
        <felem>
          <value>J</value>
          <label>Jones-Taylor-Thornton matrix</label>
          <code proglang="perl">""</code>
          <code proglang="python">""</code>
        </felem>
        <felem>
          <value>H</value>
          <label>Henikoff/Tillier PMB matrix</label>
          <code proglang="perl">"P\\n"</code>
          <code proglang="python">"P\n"</code>
        </felem>
        <felem>
          <value>D</value>
          <label>Dayhoff PAM matrix</label>
          <code proglang="perl">"P\\nP\\n"</code>
          <code proglang="python">"P\nP\n"</code>
        </felem>
        <felem>
          <value>K</value>
          <label>Kimura formula</label>
          <code proglang="perl">"P\\nP\\nP\\n"</code>
          <code proglang="python">"P\nP\nP\n"</code>
        </felem>
        <felem>
          <value>S</value>
          <label>Similarity table</label>
          <code proglang="perl">"P\\nP\\nP\\nP\\n"</code>
          <code proglang="python">"P\nP\nP\nP\n"</code>
        </felem>
        <felem>
          <value>C</value>
          <label>Categories model</label>
          <code proglang="perl">"P\\nP\\nP\\nP\\nP\\n"</code>
          <code proglang="python">"P\nP\nP\nP\nP\n"</code>
        </felem>
      </flist>
      <argpos>2</argpos>
      <paramfile>protdist.params</paramfile>
    </parameter>
    <parameter ismandatory="1">
      <name>gamma_dist</name>
      <prompt lang="en">Gamma distribution of rates among positions (G)</prompt>
      <type>
        <datatype>
          <class>Choice</class>
        </datatype>
      </type>
      <precond>
        <code proglang="perl">$Method =~ /^[JDC]$/</code>
        <code proglang="python">Method in [ "J" , "D" , "C" ]</code>
      </precond>
      <vdef>
        <value>N</value>
      </vdef>
      <flist>
        <felem>
          <value>N</value>
          <label>No</label>
          <code proglang="perl">""</code>
          <code proglang="python">""</code>
        </felem>
        <felem>
          <value>Y</value>
          <label>Yes</label>
          <code proglang="perl">"G\\n"</code>
          <code proglang="python">"G\n"</code>
        </felem>
        <felem>
          <value>G</value>
          <label>Gamma+Invariant</label>
          <code proglang="perl">"G\\nG\\n"</code>
          <code proglang="python">"G\nG\n"</code>
        </felem>
      </flist>
      <argpos>2</argpos>
      <paramfile>protdist.params</paramfile>
    </parameter>
    <parameter ismandatory="1">
      <name>gamma</name>
      <prompt lang="en">Coefficient of variation of substitution rate among positions (must be positive)</prompt>
      <type>
        <datatype>
          <class>Float</class>
        </datatype>
      </type>
      <precond>
        <code proglang="perl">$gamma_dist =~ /^[YG]$/</code>
        <code proglang="python">gamma_dist in [ "Y" , "G" ]</code>
      </precond>
      <format>
        <code proglang="perl">"$value\\n"</code>
        <code proglang="python">str( value )+ "\n"</code>
      </format>
      <argpos>1500</argpos>
      <comment>
        <text lang="en">
          Instead of the more widely-known coefficient alpha, PROTDIST uses the coefficient of variation (ratio of the standard deviation to the mean) of rates among amino acid positions. So if there is 20% variation in rates, the CV is is 0.20. The square of the C.V. is also the reciprocal of the better-known shape parameter, alpha, of the Gamma distribution, so in this case the shape parameter alpha = 1/(0.20*0.20) = 25. If you want to achieve a particular value of alpha, such as 10, you will want to use a CV of 1/sqrt(100) = 1/10 = 0.1.
        </text>
      </comment>
      <paramfile>protdist.params</paramfile>
    </parameter>
    <parameter ismandatory="1">
      <name>invariant</name>
      <prompt>Fraction of invariant positions</prompt>
      <type>
        <datatype>
          <class>Float</class>
        </datatype>
      </type>
      <precond>
        <code proglang="perl">$gamma_dist eq "G"/</code>
        <code proglang="python">gamma_dist == "G"</code>
      </precond>
      <format>
        <code proglang="perl">"$value\\n"</code>
        <code proglang="python">str(value)+"\n"</code>
      </format>
      <argpos>1501</argpos>
      <paramfile>protdist.params</paramfile>
    </parameter>
    <paragraph>
      <name>bootstrap</name>
      <prompt lang="en">Bootstrap options</prompt>
      <parameters>
        <parameter issimple="1">
          <name>seqboot</name>
          <prompt lang="en">Perform a bootstrap before analysis</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="perl">($value) ? "seqboot &lt; seqboot.params &amp;&amp; mv outfile seqboot.outfile &amp;&amp; rm infile  &amp;&amp; ln -s seqboot.outfile infile &amp;&amp; " : ""</code>
            <code proglang="python">( "" , "seqboot &lt; seqboot.params &amp;&amp; mv outfile seqboot.outfile &amp;&amp; rm infile &amp;&amp; ln -s seqboot.outfile infile &amp;&amp; " )[ value ]</code>
          </format>
          <argpos>-5</argpos>
          <comment>
            <text lang="en">By selecting this option, the bootstrap will be performed on your sequence file. So you don't need to perform a separated seqboot before.</text>
            <text lang="en">Don't give an already bootstrapped file to the program, this won't work!</text>
          </comment>
        </parameter>
        <parameter ismandatory="1" issimple="1">
          <name>resamp_method</name>
          <prompt lang="en">Resampling methods (J)</prompt>
          <type>
            <datatype>
              <class>Choice</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$seqboot</code>
            <code proglang="python">seqboot</code>
          </precond>
          <vdef>
            <value>bootstrap</value>
          </vdef>
          <flist>
            <felem>
              <value>bootstrap</value>
              <label>Bootstrap</label>
              <code proglang="perl">""</code>
              <code proglang="python">""</code>
            </felem>
            <felem>
              <value>jackknife</value>
              <label>Delete-half jackknife</label>
              <code proglang="perl">"J\\n"</code>
              <code proglang="python">""</code>
            </felem>
            <felem>
              <value>permute_species</value>
              <label>Permute species for each character</label>
              <code proglang="perl">"J\\nJ\\n"</code>
              <code proglang="python">"J\nJ\n"</code>
            </felem>
            <felem>
              <value>permute_char</value>
              <label>Permute character order</label>
              <code proglang="perl">"J\\nJ\\nJ\\n"</code>
              <code proglang="python">"J\nJ\nJ\n"</code>
            </felem>
            <felem>
              <value>permute_within_species</value>
              <label>Permute within species</label>
              <code proglang="perl">"J\\nJ\\nJ\\nJ\\n"</code>
              <code proglang="python">"J\nJ\nJ\nJ\n"</code>
            </felem>
          </flist>
          <argpos>1</argpos>
          <comment>
            <text lang="en">
              1. The bootstrap. Bootstrapping was invented by Bradley Efron in 1979, and its use in phylogeny estimation was introduced by me (Felsenstein, 1985b). It involves creating a new data set by sampling N characters randomly with replacement, so that the resulting data set has the same size as the original, but some characters have been left out and others are duplicated. The random variation of the results from analyzing these bootstrapped data sets can be shown statistically to be
              typical of the variation that you would get from collecting new data sets. The method assumes that the characters evolve independently, an assumption that may not be realistic for many kinds of data.
            </text>
            <text lang="en">
              2. Delete-half-jackknifing. This alternative to the bootstrap involves sampling a random half of the characters, and including them in the data but dropping the others. The resulting data sets are half the size of the original, and no characters are duplicated. The random variation from doing this should be very similar to that obtained from the bootstrap. The method is advocated by Wu (1986).
            </text>
            <text lang="en">
              3. Permuting species for each characters. This method of resampling (well, OK, it may not be best to call it resampling) was introduced by Archie (1989) and Faith (1990; see also Faith and Cranston, 1991). It involves permuting the columns of the data matrix separately. This produces data matrices that have the same number and kinds of characters but no taxonomic structure. It is used for different purposes than the bootstrap, as it tests not the variation around an estimated tree but the hypothesis that there is no taxonomic structure in the data: if a statistic such as number of steps is significantly smaller in the actual data than it is in replicates that are permuted, then we can argue that there is some taxonomic structure in the data (though perhaps it might be just the presence of aa pair of sibling species).
            </text>
            <text lang="en">
              4. Permuting characters order. This simply permutes the order of the characters, the same reordering being applied to all species. For many methods of tree inference this will make no difference to the outcome (unless one has rates of evolution correlated among adjacent sites). It is included as a possible step in carrying out a permutation test of homogeneity of characters (such as the Incongruence Length Difference test).
            </text>
            <text lang="en">
              5. Permuting characters separately for each species. This is a method introduced by Steel, Lockhart, and Penny (1993) to permute data so as to destroy all phylogenetic structure, while keeping the base composition of each species the same as before. It shuffles the character order separately for each species.
            </text>
          </comment>
          <paramfile>seqboot.params</paramfile>
        </parameter>
        <parameter ismandatory="1" issimple="1">
          <name>seqboot_seed</name>
          <prompt lang="en">Random number seed (must be odd)</prompt>
          <type>
            <datatype>
              <class>Integer</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$seqboot</code>
            <code proglang="python">seqboot</code>
          </precond>
          <format>
            <code proglang="perl">"$value\\n"</code>
            <code proglang="python">str( value ) + "\n"</code>
          </format>
          <ctrl>
            <message>
              <text lang="en">Random number seed must be odd</text>
            </message>
            <code proglang="perl">$value &gt; 0 and ($value % 2) != 0</code>
            <code proglang="python">value &gt; 0 and (value % 2) != 0</code>
          </ctrl>
          <argpos>10000</argpos>
          <paramfile>seqboot.params</paramfile>
        </parameter>
        <parameter issimple="1">
          <name>replicates</name>
          <prompt lang="en">How many replicates (R)?</prompt>
          <type>
            <datatype>
              <class>Integer</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$seqboot</code>
            <code proglang="python">seqboot</code>
          </precond>
          <vdef>
            <value>100</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value != $vdef) ? "R\\n$value\\n" : ""</code>
            <code proglang="python">( "", "R\n" +str( value )+ "\n" )[ value is not None and value != vdef ]</code>
          </format>
          <ctrl>
            <message>
              <text lang="en">This server allows no more than 1000 replicates</text>
            </message>
            <code proglang="perl">$replicates &lt;= 1000</code>
            <code proglang="python">replicates &lt;= 1000</code>
          </ctrl>
          <ctrl>
            <message>
              <text lang="en">Bad data sets number:  it must be greater than 1</text>
            </message>
            <code proglang="perl">$value &gt; 1</code>
            <code proglang="python">value &gt; 1</code>
          </ctrl>
          <argpos>1</argpos>
          <paramfile>seqboot.params</paramfile>
        </parameter>
      </parameters>
    </paragraph>
    <paragraph>
      <name>weight_opt</name>
      <prompt lang="en">Weight options</prompt>
      <parameters>
        <parameter>
          <name>weights</name>
          <prompt lang="en">Use weights for sites (W)</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="perl">($value) ? "W\\n" : ""</code>
            <code proglang="python">( "" , "W\n" )[ value ]</code>
          </format>
          <argpos>1</argpos>
          <paramfile>protdist.params</paramfile>
        </parameter>
        <parameter ismandatory="1">
          <name>weights_file</name>
          <prompt lang="en">Weights file</prompt>
          <type>
            <datatype>
              <class>PhylipWeight</class>
              <superclass>AbstractText</superclass>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$weights</code>
            <code proglang="python">weights</code>
          </precond>
          <format>
            <code proglang="perl">(defined $value) ? "ln -s $weights_file weights &amp;&amp; " : ""</code>
            <code proglang="python">( "" , "ln -s " + str( weights_file ) + " weights &amp;&amp; " )[ value is not None ]</code>
          </format>
          <ctrl>
            <message>
              <text lang="en">the name of this data can't be "infile" or "outfile"</text>
            </message>
            <code proglang="python">value not in ( "infile" , "outfile" )</code>
            <code proglang="perl">$value ne "infile" and $value ne "outfile"</code>
          </ctrl>
          <argpos>-1</argpos>
        </parameter>
      </parameters>
    </paragraph>
    <parameter ishidden="1">
      <name>multiple_dataset</name>
      <type>
        <datatype>
          <class>String</class>
        </datatype>
      </type>
      <precond>
        <code proglang="perl">$seqboot and $replicates &gt; 1 </code>
        <code proglang="python">seqboot and replicates &gt; 1 </code>
      </precond>
      <format>
        <code proglang="perl">"M\\nD\\n$replicates\\n"</code>
        <code proglang="python">"M\nD\n"+ str( replicates ) + "\n"</code>
      </format>
      <argpos>1</argpos>
      <paramfile>protdist.params</paramfile>
    </parameter>
    <parameter ishidden="1">
      <name>bootconfirm</name>
      <type>
        <datatype>
          <class>String</class>
        </datatype>
      </type>
      <precond>
        <code proglang="perl">$seqboot</code>
        <code proglang="python">seqboot</code>
      </precond>
      <format>
        <code proglang="perl">"Y\\n"</code>
        <code proglang="python">"Y\n"</code>
      </format>
      <argpos>1000</argpos>
      <paramfile>seqboot.params</paramfile>
    </parameter>
    <parameter ishidden="1">
      <name>bootterminal_type</name>
      <type>
        <datatype>
          <class>String</class>
        </datatype>
      </type>
      <precond>
        <code proglang="perl">$seqboot</code>
        <code proglang="python">seqboot</code>
      </precond>
      <format>
        <code proglang="perl">"0\\n"</code>
        <code proglang="python">"0\n"</code>
      </format>
      <argpos>-1</argpos>
      <paramfile>seqboot.params</paramfile>
    </parameter>
    <paragraph>
      <name>output</name>
      <prompt lang="en">Output options</prompt>
      <parameters>
        <parameter>
          <name>printdata</name>
          <prompt lang="en">Print out the data at start of run (1)</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="perl">($value) ? "1\\n" : ""</code>
            <code proglang="python">( "" , "1\n" )[ value ]</code>
          </format>
          <argpos>1</argpos>
          <paramfile>protdist.params</paramfile>
        </parameter>
      </parameters>
    </paragraph>
    <paragraph>
      <name>categ_options</name>
      <prompt lang="en">Categories model options (options available only if Categories model choosed)</prompt>
      <precond>
        <code proglang="perl">$Method eq "C"</code>
        <code proglang="python">Method == "C"</code>
      </precond>
      <argpos>3</argpos>
      <parameters>
        <parameter>
          <name>code</name>
          <prompt lang="en">Genetic code (U)</prompt>
          <type>
            <datatype>
              <class>Choice</class>
            </datatype>
          </type>
          <vdef>
            <value>U</value>
          </vdef>
          <vlist>
            <velem>
              <value>U</value>
              <label>Universal (U)</label>
            </velem>
            <velem>
              <value>M</value>
              <label>Mitochondrial (M)</label>
            </velem>
            <velem>
              <value>V</value>
              <label>Vertebrate mitochondrial (V)</label>
            </velem>
            <velem>
              <value>F</value>
              <label>Fly mitochondrial (F)</label>
            </velem>
            <velem>
              <value>Y</value>
              <label>Yeast mitochondrial (Y)</label>
            </velem>
          </vlist>
          <format>
            <code proglang="perl">(defined $value and $value ne $vdef) ? "U\\n$code\\n" : ""</code>
            <code proglang="python">( "", "U\n" + str( code ) + "\n" )[ value is not None and value != vdef ]</code>
          </format>
          <argpos>3</argpos>
          <paramfile>protdist.params</paramfile>
        </parameter>
        <parameter>
          <name>categorization</name>
          <prompt lang="en">Categorization of amino acids (A)</prompt>
          <type>
            <datatype>
              <class>Choice</class>
            </datatype>
          </type>
          <vdef>
            <value>G</value>
          </vdef>
          <vlist>
            <velem>
              <value>G</value>
              <label>George/Hunt/Barker (G)</label>
            </velem>
            <velem>
              <value>C</value>
              <label>Chemical (C)</label>
            </velem>
            <velem>
              <value>H</value>
              <label>Hall (H)</label>
            </velem>
          </vlist>
          <format>
            <code proglang="perl">(defined $value and $value ne $vdef) ? "A\\n$categorization\\n" : ""</code>
            <code proglang="python">( "" , "A\n" +str( categorization ) +"\n" )[ value is not None and value != vdef ]</code>
          </format>
          <argpos>10</argpos>
          <comment>
            <text lang="en">All have groups: (Glu Gln Asp Asn), (Lys Arg His), (Phe Tyr Trp) plus:</text>
            <text lang="en">George/Hunt/Barker: (Cys), (Met Val Leu Ileu), (Gly Ala Ser Thr Pro)</text>
            <text lang="en">Chemical: (Cys Met), (Val Leu Ileu Gly Ala Ser Thr), (Pro)</text>
            <text lang="en">Hall: (Cys), (Met Val Leu Ileu), (Gly Ala Ser Thr), (Pro)</text>
          </comment>
          <paramfile>protdist.params</paramfile>
        </parameter>
        <parameter>
          <name>change_prob</name>
          <prompt lang="en">Prob change category (1.0=easy) (E)</prompt>
          <type>
            <datatype>
              <class>Float</class>
            </datatype>
          </type>
          <vdef>
            <value>0.4570</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value != $vdef) ? "E\\n$value\\n" : ""</code>
            <code proglang="python">("", "E\n"+ str( value ) +"\n")[ value is not None and value != vdef ]</code>
          </format>
          <ctrl>
            <message>
              <text lang="en">Enter a value between 0.0 and 1.0</text>
            </message>
            <code proglang="perl">$change_prob &gt; 0.0 and $change_prob &lt; 1.0</code>
            <code proglang="python">change_prob &gt; 0.0 and change_prob &lt; 1.0</code>
          </ctrl>
          <argpos>3</argpos>
          <paramfile>protdist.params</paramfile>
        </parameter>
        <parameter>
          <name>ratio</name>
          <prompt lang="en">Transition/transversion ratio (T)</prompt>
          <type>
            <datatype>
              <class>Float</class>
            </datatype>
          </type>
          <vdef>
            <value>2.000</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value != $vdef) ? "T\\n$value\\n" : ""</code>
            <code proglang="python">("", "T\n"+str(value)+"\n")[value is not None and value != vdef]</code>
          </format>
          <ctrl>
            <message>
              <text lang="en">The transition/transversion ratio must be any number from 0.5 upwards.</text>
            </message>
            <code proglang="python">value &gt;= 0.5</code>
            <code proglang="perl"> $value &gt;= 0.5</code>
          </ctrl>
          <argpos>3</argpos>
          <comment>
            <text lang="en">If the Categories distance is selected another menu option, T,
             will appear allowing the user to supply the Transition/Transversion ratio that should be assumed at the underlying DNA level.
             The transition/transversion ratio can be any number from 0.5 upwards.</text>
          </comment>
          <paramfile>protdist.params</paramfile>
        </parameter>
      </parameters>
    </paragraph>
    <parameter isout="1">
      <name>outfile</name>
      <prompt lang="en">Outfile</prompt>
      <type>
        <datatype>
          <class>PhylipDistanceMatrix</class>
          <superclass>AbstractText</superclass>
        </datatype>
      </type>
      <format>
        <code proglang="perl">" &amp;&amp; mv outfile protdist.outfile"</code>
        <code proglang="python">" &amp;&amp; mv outfile protdist.outfile"</code>
      </format>
      <argpos>40</argpos>
      <filenames>
        <code proglang="perl">"protdist.outfile"</code>
        <code proglang="python">"protdist.outfile"</code>
      </filenames>
    </parameter>
    <parameter isout="1">
      <name>seqboot_out</name>
      <prompt lang="en">seqboot outfile</prompt>
      <type>
        <datatype>
          <class>SetOfAlignment</class>
          <superclass>AbstractText</superclass>
        </datatype>
      </type>
      <precond>
        <code proglang="perl">$seqboot</code>
        <code proglang="python">seqboot</code>
      </precond>
      <argpos>40</argpos>
      <filenames>
        <code proglang="perl">"seqboot.outfile"</code>
        <code proglang="python">"seqboot.outfile"</code>
      </filenames>
    </parameter>
    <parameter ishidden="1">
      <name>confirm</name>
      <type>
        <datatype>
          <class>String</class>
        </datatype>
      </type>
      <format>
        <code proglang="perl">"Y\\n"</code>
        <code proglang="python">"Y\n"</code>
      </format>
      <argpos>1000</argpos>
      <paramfile>protdist.params</paramfile>
    </parameter>
    <parameter ishidden="1">
      <name>terminal_type</name>
      <type>
        <datatype>
          <class>String</class>
        </datatype>
      </type>
      <format>
        <code proglang="perl">"0\\n"</code>
        <code proglang="python">"0\n"</code>
      </format>
      <argpos>-1</argpos>
      <paramfile>protdist.params</paramfile>
    </parameter>
  </parameters>
</program>