/var/lib/mobyle/programs/dnadist.xml is in mobyle-programs 5.1.2-2.
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<!-- 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>dnadist</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/phylip_package.xml"/>
<doc>
<title>dnadist</title>
<description>
<text lang="en">Compute distance matrix from nucleotide sequences</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/phylip/doc/dnadist.html</doclink>
<comment>
<text lang="en">This program uses nucleotide sequences to compute a distance matrix, under four different models of nucleotide substitution. It can also
compute a table of similarity between the nucleotide sequences. 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>dnadist</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"dnadist <dnadist.params"</code>
<code proglang="python">"dnadist <dnadist.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>DNA</biotype>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>PHYLIPI</dataFormat>
</type>
<format>
<code proglang="perl">"ln -s $infile infile && "</code>
<code proglang="python">"ln -s " + str( infile ) + " infile && "</code>
</format>
<ctrl>
<message>
<text lang="en">the name of this data can't be "infile" or "outfile"</text>
</message>
<code proglang="python">value not in ( "infile" , "outfile" )</code>
<code proglang="perl">$value ne "infile" and $value ne "outfile"</code>
</ctrl>
<argpos>-10</argpos>
<comment>
<text lang="en">The input file must contained aligned sequences in PHYLIP format obtained by sequence alignment programs.</text>
</comment>
<example>
5 13
Alpha AACGTGGCCACAT
Beta AAGGTCGCCACAC
Gamma CAGTTCGCCACAA
Delta GAGATTTCCGCCT
Epsilon GAGATCTCCGCCC
</example>
</parameter>
<paragraph>
<name>dnadist_opt</name>
<prompt lang="en">Dnadist options</prompt>
<parameters>
<parameter>
<name>distance</name>
<prompt lang="en">Distance (D)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>F84</value>
</vdef>
<flist>
<felem>
<value>F84</value>
<label>F84</label>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</felem>
<felem>
<value>K</value>
<label>Kimura 2-parameter</label>
<code proglang="perl">"D\\n"</code>
<code proglang="python">"D\n"</code>
</felem>
<felem>
<value>JC</value>
<label>Jukes-Cantor</label>
<code proglang="perl">"D\\nD\\n"</code>
<code proglang="python">"D\nD\n"</code>
</felem>
<felem>
<value>LogDet</value>
<label>LogDet</label>
<code proglang="perl">"D\\nD\\nD\\n"</code>
<code proglang="python">"D\nD\nD\n"</code>
</felem>
<felem>
<value>Similarity</value>
<label>Similarity table</label>
<code proglang="perl">"D\\nD\\nD\\nD\\n"</code>
<code proglang="python">"D\nD\nD\nD\n"</code>
</felem>
</flist>
<argpos>1</argpos>
<paramfile>dnadist.params</paramfile>
</parameter>
<parameter>
<name>ratio</name>
<prompt lang="en">Transition/transversion ratio (T)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$distance eq "F84" or $distance eq "K"</code>
<code proglang="python">distance == "F84" or distance == "K"</code>
</precond>
<vdef>
<value>2.0</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">Transition/transversion ratio (T) must be a real number greater than 0.0</text>
</message>
<code proglang="python">value >= 0.0</code>
<code proglang="perl">$value >= 0.0</code>
</ctrl>
<argpos>1</argpos>
<comment>
<text lang="en">The T option in this program does not stand for Threshold, but instead is the Transition/transversion option.
The user is prompted for a real number greater than 0.0, as the expected ratio of transitions to transversions.
Note that this is not the ratio of the first to the second kinds of events, but the resulting expected ratio of transitions to transversions.
The exact relationship between these two quantities depends on the frequencies in the base pools.
The default value of the T parameter if you do not use the T option is 2.0.</text>
</comment>
<paramfile>dnadist.params</paramfile>
</parameter>
<parameter>
<name>gamma</name>
<prompt lang="en">Gamma distributed rates across sites (G)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">$distance eq "F84" or $distance eq "K" or $distance eq "JC"</code>
<code proglang="python">distance == "F84" or distance == "K" or distance == "JC"</code>
</precond>
<vdef>
<value>No</value>
</vdef>
<flist>
<felem>
<value>No</value>
<label>No</label>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</felem>
<felem>
<value>1</value>
<label>Yes</label>
<code proglang="perl">"G\\n"</code>
<code proglang="python">"G\n"</code>
</felem>
<felem>
<value>GI</value>
<label>Gamma+Invariant</label>
<code proglang="perl">"G\\nG\\n"</code>
<code proglang="python">"G\nG\n"</code>
</felem>
</flist>
<argpos>5</argpos>
<paramfile>dnadist.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>variation_coeff</name>
<prompt lang="en">Coefficient of variation of substitution rate among sites (must be positive) (if Gamma)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$gamma ne "No"</code>
<code proglang="python">gamma != "No"</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? "$value\\n" : ""</code>
<code proglang="python">( "" , str( value ) + "\n" )[ value is not None ]</code>
</format>
<argpos>1010</argpos>
<comment>
<text lang="en">In gamma distribution parameters, this is 1/(square root of alpha)</text>
</comment>
<paramfile>dnadist.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>invariant_sites</name>
<prompt lang="en">Fraction of invariant sites (if Gamma)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$gamma eq "GI"</code>
<code proglang="python">gamma == "GI"</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? "$value\\n" : ""</code>
<code proglang="python">( "" , str( value ) + "\n" )[ value is not None ]</code>
</format>
<argpos>1011</argpos>
<paramfile>dnadist.params</paramfile>
</parameter>
<paragraph>
<name>ACGT_frequencies</name>
<prompt lang="en">Base frequencies for A, C, G, T/U (if not empirical)</prompt>
<precond>
<code proglang="perl">distance eq "F84"</code>
<code proglang="python">distance == "F84"</code>
</precond>
<comment>
<text lang="en">These must add to 1</text>
</comment>
<parameters>
<parameter>
<name>empirical_frequencies</name>
<prompt lang="en">Use empirical base frequencies (F)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<argpos>1</argpos>
<paramfile>dnadist.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>A_frequency</name>
<prompt lang="en">Base frequencies for A</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $empirical_frequencies</code>
<code proglang="python">not empirical_frequencies</code>
</precond>
<vdef>
<value>0.25</value>
</vdef>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
<argpos>2</argpos>
</parameter>
<parameter ismandatory="1">
<name>C_frequency</name>
<prompt lang="en">Base frequencies for C</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $empirical_frequencies</code>
<code proglang="python">not empirical_frequencies</code>
</precond>
<vdef>
<value>0.25</value>
</vdef>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
<argpos>2</argpos>
</parameter>
<parameter ismandatory="1">
<name>G_frequency</name>
<prompt lang="en">Base frequencies for G</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $empirical_frequencies</code>
<code proglang="python">not empirical_frequencies</code>
</precond>
<vdef>
<value>0.25</value>
</vdef>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
<argpos>2</argpos>
</parameter>
<parameter ismandatory="1">
<name>T_frequency</name>
<prompt lang="en">Base frequencies for T/U</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $empirical_frequencies</code>
<code proglang="python">not empirical_frequencies</code>
</precond>
<vdef>
<value>0.25</value>
</vdef>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
<argpos>2</argpos>
</parameter>
<parameter ishidden="1">
<name>base_frequencies</name>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $empirical_frequencies</code>
<code proglang="python">not empirical_frequencies</code>
</precond>
<format>
<code proglang="perl">"F\\n$A_frequency $C_frequency $G_frequency $T_frequency\\n"</code>
<code proglang="python">"F\n" + str( A_frequency ) + " " + str( C_frequency ) + " " + str( G_frequency ) + " " + str( T_frequency ) + "\n"</code>
</format>
<argpos>2</argpos>
<paramfile>dnadist.params</paramfile>
</parameter>
</parameters>
</paragraph>
</parameters>
</paragraph>
<paragraph>
<name>weight_opt</name>
<prompt lang="en">Weight options</prompt>
<parameters>
<parameter>
<name>weights</name>
<prompt lang="en">Use weights for sites (W)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "W\\n" : ""</code>
<code proglang="python">( "" , "W\n" )[ value ]</code>
</format>
<argpos>1</argpos>
<paramfile>dnadist.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 $weights_file weights && " : ""</code>
<code proglang="python">( "" , " ln -s " + str( weights_file ) + " weights && " )[ value is not None]</code>
</format>
<ctrl>
<message>
<text lang="en">the name of this data can't be "infile" or "outfile"</text>
</message>
<code proglang="python">value not in ( "infile" , "outfile" )</code>
<code proglang="perl">$value ne "infile" and $value ne "outfile"</code>
</ctrl>
<argpos>-1</argpos>
<comment>
<text lang="en">It selects a set of sites to be analyzed, ignoring the others.
The sites selected are those with weight 1.
The weights in it are a simple string of digits.
Blanks in the weightfile are skipped over and ignored, and the weights can continue to a new line.</text>
</comment>
<example>1011001001011</example>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>bootstrap</name>
<prompt lang="en">Bootstrap options</prompt>
<parameters>
<parameter issimple="1">
<name>seqboot</name>
<prompt lang="en">Perform a bootstrap before analysis</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "seqboot < seqboot.params && mv outfile seqboot.outfile && rm infile && ln -s seqboot.outfile infile && " : ""</code>
<code proglang="python">( "" , "seqboot < seqboot.params && mv outfile seqboot.outfile && rm infile && ln -s seqboot.outfile infile && " )[ 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>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 >= 0 and (($value % 2) != 0)</code>
<code proglang="python">value >= 0 and ( ( value % 2 ) != 0 )</code>
</ctrl>
<argpos>1000</argpos>
<paramfile>seqboot.params</paramfile>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>replicates</name>
<prompt lang="en">How many replicates</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$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">$value <= 1000</code>
<code proglang="python">value <= 1000</code>
</ctrl>
<ctrl>
<message>
<text lang="en">Bad data sets number: it must be greater than 1</text>
</message>
<code proglang="perl">$value > 1</code>
<code proglang="python">value > 1</code>
</ctrl>
<argpos>1</argpos>
<paramfile>seqboot.params</paramfile>
</parameter>
</parameters>
</paragraph>
<!-- remove this parameter until we upgrade Phylip in ver >= 3.68 (there is a bug in lower triangular matrix)
<paragraph>
<name>output</name>
<prompt lang="en">Output options</prompt>
<parameters>
<parameter>
<name>matrix_form</name>
<prompt lang="en">form of distance matrix (L)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>square</value>
</vdef>
<flist>
<felem>
<value>square</value>
<label>Square</label>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</felem>
<felem>
<value>human_redable</value>
<label>Human-readable</label>
<code proglang="perl">"L\\n"</code>
<code proglang="python">"L\n"</code>
</felem>
<felem>
<value>lower_triangular</value>
<label>Lower-triangular</label>
<code proglang="perl">"L\\nL\\n"</code>
<code proglang="python">"L\nL\n"</code>
</felem>
</flist>
<argpos>1</argpos>
<paramfile>dnadist.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">" && mv outfile dnadist.outfile"</code>
<code proglang="python">" && mv outfile dnadist.outfile"</code>
</format>
<argpos>40</argpos>
<filenames>
<code proglang="perl">"dnadist.outfile"</code>
<code proglang="python">"dnadist.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">$seqboot</code>
<code proglang="python">seqboot</code>
</precond>
<argpos>40</argpos>
<filenames>
<code proglang="perl">"seqboot.outfile"</code>
<code proglang="python">"seqboot.outfile"</code>
</filenames>
</parameter>
<parameter ishidden="1">
<name>confirm</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"y\\n"</code>
<code proglang="python">"y\n"</code>
</format>
<argpos>1000</argpos>
<paramfile>dnadist.params</paramfile>
</parameter>
<parameter ishidden="1">
<name>terminal_type</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"0\\n"</code>
<code proglang="python">"0\n"</code>
</format>
<argpos>-1</argpos>
<paramfile>dnadist.params</paramfile>
</parameter>
<parameter ishidden="1">
<name>multiple_dataset</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="perl">$seqboot and $replicates > 1 </code>
<code proglang="python">seqboot and replicates > 1</code>
</precond>
<format>
<code proglang="perl">"M\\nD\\n$replicates\\n"</code>
<code proglang="python">"M\nD\n" + str( replicates ) + str("\n")</code>
</format>
<argpos>1</argpos>
<paramfile>dnadist.params</paramfile>
</parameter>
<parameter ishidden="1">
<name>seqboot_confirm</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="perl">$seqboot</code>
<code proglang="python">seqboot</code>
</precond>
<format>
<code proglang="perl">"y\\n"</code>
<code proglang="python">"y\n"</code>
</format>
<argpos>100</argpos>
<paramfile>seqboot.params</paramfile>
</parameter>
<parameter ishidden="1">
<name>seqboot_terminal_type</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="perl">$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>
</parameters>
</program>
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