/var/lib/mobyle/programs/dialign.xml is in mobyle-programs 5.1.2-1.
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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>dialign</name>
<version>2.2.1</version>
<doc>
<title>DIALIGN</title>
<description>
<text lang="en">DNA and protein sequence alignment based on segment-to-segment comparison</text>
</description>
<authors>Morgenstern, Dress, Werner</authors>
<reference>B. Morgenstern (1999). DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 15, 211 - 218.</reference>
<homepagelink>http://dialign.gobics.de/</homepagelink>
<sourcelink>http://dialign.gobics.de/download/</sourcelink>
</doc>
<category>alignment:multiple</category>
<command>dialign</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>sequence</name>
<prompt lang="en">Sequences</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
<card>2,n</card>
</type>
<format>
<code proglang="perl">" $value"</code>
<code proglang="python">" " + str(value)</code>
</format>
<argpos>100</argpos>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>protein_dna</name>
<prompt lang="en">Nucleic acid or protein alignment (-n)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>p</value>
</vdef>
<vlist>
<velem>
<value>p</value>
<label>Protein (p)</label>
</velem>
<velem>
<value>n</value>
<label>Nucleic (n)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -n" : ""</code>
<code proglang="python">( "" , " -n" )[ value is not None and value != vdef]</code>
</format>
<argpos>2</argpos>
</parameter>
<paragraph>
<name>dialign_opt</name>
<prompt lang="en">Others options</prompt>
<argpos>3</argpos>
<parameters>
<parameter>
<name>threshold</name>
<prompt lang="en">Threshold (-thr)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0.0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -thr $value" : ""</code>
<code proglang="python">( "" , " -thr " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>cluster</name>
<prompt lang="en">Clustering type used to construct sequence tree</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>null</value>
</vdef>
<vlist>
<velem undef="1">
<value>null</value>
<label>UPGMA</label>
</velem>
<velem>
<value>max_link</value>
<label>Maximum linkage (-max_link)</label>
</velem>
<velem>
<value>min_link</value>
<label>Minimum linkage (-min_link)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " -$value" : ""</code>
<code proglang="python">( "" , " -" +str(value) )[ value is not None and value !=vdef]</code>
</format>
<comment>
<text lang="en">"maximum or minimum linkage" clustering used to construct sequence tree (instead of UPGMA).</text>
</comment>
</parameter>
<parameter>
<name>iterative</name>
<prompt lang="en">Iterative scoring scheme (-it)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -it" : ""</code>
<code proglang="python">( "" , " -it" )[ value ]</code>
</format>
<comment>
<text lang="en">iterative scoring scheme (fragment scores are based on
conditional probabilities given the previously aligned
fragments. I.e. the probability of a fragment -- and
therefore its score -- is not based on the probability
of random occurrence in the input sequences but rather on
the probability of occurrence between those fragments
that have already been accepted in previous iteration
steps).</text>
</comment>
</parameter>
<parameter>
<name>overlap</name>
<prompt lang="en">Overlap weights (-iw)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -iw" : ""</code>
<code proglang="python">( "" , " -iw" )[ value ]</code>
</format>
<comment>
<text lang="en">overlap weights switched off (by default,
overlap weights are used if up to 35 sequences are
aligned). This option speeds up the alignment but may lead
to reduced alignment quality.</text>
</comment>
</parameter>
<paragraph>
<name>dna_opt</name>
<prompt lang="en">DNA options</prompt>
<precond>
<code proglang="perl">$protein_dna eq "n"</code>
<code proglang="python">protein_dna == "n"</code>
</precond>
<parameters>
<parameter>
<name>translation</name>
<prompt lang="en">Translation of nucleotide diagonals into peptide diagonals (-nt)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -nt" : ""</code>
<code proglang="python">( "" , " -nt" )[ value ]</code>
</format>
<comment>
<text lang="en">Input sequences are nucleic acid sequences and `nucleic acid segments' are translated to `peptide segments'.</text>
</comment>
</parameter>
<parameter>
<name>translation_strand</name>
<prompt lang="en">Strand to looked at Watson and Crick strands (-cs)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">$translation or $mix</code>
<code proglang="python">translation or mix</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -cs" : ""</code>
<code proglang="python">( "" , " -cs" )[ value ]</code>
</format>
<comment>
<text lang="en">If segments are translated, not only the `Watson strand' but also the `Crick strand' is looked at</text>
</comment>
</parameter>
<parameter>
<name>mix</name>
<prompt lang="en">Mixed alignments (-ma)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -ma" : ""</code>
<code proglang="python">( "" , " -ma" )[ value ]</code>
</format>
<comment>
<text lang="en">`mixed alignments' consisting of P-fragments and N-fragments if nucleic acid sequences are aligned.</text>
</comment>
</parameter>
<parameter>
<name>speed</name>
<prompt lang="en">Dna alignment speed up (-ds)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -ds" : ""</code>
<code proglang="python">( "" , " -ds" )[ value ]</code>
</format>
<comment>
<text lang="en">Non-translated nucleic acid fragments are taken
into account only if they start with at least two matches.
Speeds up DNA alignment at the expense of sensitivity.</text>
</comment>
</parameter>
<parameter>
<name>long_genomic</name>
<prompt lang="en">Long genomic sequences (-lgs)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $long_genomic_pep</code>
<code proglang="python">not long_genomic_pep</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -lgs" : ""</code>
<code proglang="python">( "" , " -lgs" )[ value ]</code>
</format>
<comment>
<text lang="en">combines the following options:
-ma, -it, -thr 2, -lmax 30, -smin 8, -nta, -ff,
-fop, -ff, -cs, -ds, -pst</text>
</comment>
</parameter>
<parameter>
<name>long_genomic_pep</name>
<prompt lang="en">Long genomic sequences (-lfs_t)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $long_genomic</code>
<code proglang="python">not long_genomic</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -lgs_t" : ""</code>
<code proglang="python">( "" , " -lgs_t" )[ value ]</code>
</format>
<comment>
<text lang="en"> Like "-lgs" but with all segment pairs assessed at the peptide level (rather than 'mixed alignments' as with the"-lgs" option). Therefore faster than -lgs but not very sensitive for non-coding regions.</text>
</comment>
</parameter>
</parameters>
</paragraph>
</parameters>
</paragraph>
<paragraph>
<name>output_options</name>
<prompt lang="en">Output options</prompt>
<argpos>3</argpos>
<parameters>
<parameter>
<name>max_simil</name>
<prompt lang="en">Maximum number of * characters representing degree similarity (-stars)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -stars $value" : ""</code>
<code proglang="python">( "" , " -stars " + str(value) )[ value is not None]</code>
</format>
<comment>
<text lang="en">The number of `*' characters below the alignment reflects the degree of local similarity among sequences. More precisely: They represent the sum of `weights' of diagonals connecting residues at the respective position.</text>
<text lang="en">By default, no stars are used but numbers between 0 and 9, instead.</text>
</comment>
</parameter>
<parameter>
<name>mask</name>
<prompt lang="en">Mask not aligned residues (-mask)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -mask" : ""</code>
<code proglang="python">( "" , " -mask" )[ value ]</code>
</format>
<comment>
<text lang="en">residues not belonging to selected fragments are replaced by `*' characters in output alignment (rather than being printed in lower-case characters)</text>
</comment>
</parameter>
<parameter>
<name>fasta</name>
<prompt lang="en">Alignment in fasta format (-fa)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -fa" : ""</code>
<code proglang="python">( "" , " -fa" )[ value ]</code>
</format>
<comment>
<text lang="en">Be aware that only upper-case letters are regarded to be aligned in fasta output file.</text>
</comment>
</parameter>
<!-- ** Invalid generated CLUSTAL format **
<parameter>
<name>clustal</name>
<prompt lang="en">Alignment in clustal format (-cw)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -cw" : ""</code>
<code proglang="python">( "" , " -cw" )[ value ]</code>
</format>
<comment>
<text lang="en">Additional output file in CLUSTAL W format.</text>
</comment>
</parameter>
** Invalid generated CLUSTAL format ** -->
</parameters>
</paragraph>
<parameter isout="1">
<name>ali</name>
<prompt>Output file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<filenames>
<code proglang="perl">"*.ali"</code>
<code proglang="perl">"*.cw"</code>
<code proglang="python">"*.ali"</code>
<code proglang="python">"*.cw"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>fasta_alignment</name>
<prompt>fasta alignment file</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>Fasta</dataFormat>
</type>
<precond>
<code proglang="perl">$fasta</code>
<code proglang="python">fasta</code>
</precond>
<filenames>
<code proglang="perl">"*.fa"</code>
<code proglang="python">"*.fa"</code>
</filenames>
</parameter>
</parameters>
</program>
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