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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>fastDNAml</name>
<version>1.2.2</version>
<doc>
<title>fastDNAml</title>
<description>
<text lang="en">Construction of phylogenetic trees of DNA sequences using maximum likelihood</text>
</description>
<authors>Olsen, Matsuda, Hagstrom, Overbeek</authors>
<reference>Olsen, G. J., Matsuda, H., Hagstrom, R., and Overbeek, R. 1994. fastDNAml: A tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput. Appl. Biosci. 10: 41-48.</reference>
<reference>Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17: 368-376.</reference>
<homepagelink>http://iubio.bio.indiana.edu/soft/molbio/evolve/fastdnaml/fastDNAml.html</homepagelink>
</doc>
<category>phylogeny:likelihood</category>
</head>
<parameters>
<parameter iscommand="1" ishidden="1">
<name>fastdnaml</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">($bootstrap) ? "cat > $infile.tmp;" : "fastDNAml"</code>
<code proglang="python">("fastDNAml", "cat > %s.tmp;" % infile )[bootstrap]</code>
</format>
<argpos>1000</argpos>
</parameter>
<parameter ishidden="1">
<name>clean_tmp</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">" && clean_checkpoints"</code>
<code proglang="python">" && clean_checkpoints"</code>
</format>
<argpos>1100</argpos>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>infile</name>
<prompt lang="en">Sequence Alignment File</prompt>
<type>
<biotype>DNA</biotype>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>PHYLIPI</dataFormat>
</type>
<format>
<code proglang="perl">"cat $value | "</code>
<code proglang="python">"cat " + str(value) + " | "</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">The input to fastDNAml is similar to that used by DNAML (and the other PHYLIP programs). At least 3 sequences are required.</text>
</comment>
</parameter>
<paragraph>
<name>inputopt</name>
<prompt lang="en">Input Options</prompt>
<parameters>
<parameter>
<name>frequencies</name>
<prompt lang="en">Use empirical base frequencies derived from the sequence data ?</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(not $value and not ($fA and $fC and $fG and $fT )) ? "": "frequencies $fA $fC $fG $fT | "</code>
<code proglang="python">( "" ,"frequencies %s %s %s %s | " % (str(fA), str(fC), str(fG), str(fT)) )[ not ( value and fA is None and fC is None and fG is None and fT is None) ]</code>
</format>
<argpos>2</argpos>
</parameter>
<paragraph>
<name>user_frequencies</name>
<prompt lang="en">User bases frequencies (instead of empirical frequencies)</prompt>
<precond>
<code proglang="perl">not $frequencies</code>
<code proglang="python">not frequencies</code>
</precond>
<parameters>
<parameter ismandatory="1">
<name>fA</name>
<prompt lang="en">A frequency</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
</parameter>
<parameter ismandatory="1">
<name>fC</name>
<prompt lang="en">C frequency</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
</parameter>
<parameter ismandatory="1">
<name>fG</name>
<prompt lang="en">G frequency</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
</parameter>
<parameter ismandatory="1">
<name>fT</name>
<prompt lang="en">T frequency</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
</parameter>
</parameters>
</paragraph>
<parameter>
<name>transition</name>
<prompt lang="en">Transition/transversion ratio</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>2.0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value!=$vdef) ? " transition $value | " : ""</code>
<code proglang="python">( "" , " transition " + str(value) + " | " )[ value is not None and value != vdef]</code>
</format>
<argpos>10</argpos>
<comment>
<text lang="en">This option can be used before a global or treefile option with auxiliary data.</text>
</comment>
</parameter>
<parameter>
<name>jumble</name>
<prompt lang="en">Randomize input order of sequences (jumble)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $bootstrap</code>
<code proglang="python">not bootstrap</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "jumble | " : ""</code>
<code proglang="python">( "" , "jumble | " )[ value ]</code>
</format>
<argpos>10</argpos>
<comment>
<text lang="en">
Note that fastDNAml explores a very small number of alternative tree topologies relative to a typical parsimony program. There is a very real chance that the search procedure will not find the tree topology with the highest likelihood. Altering the order of taxon addition and comparing the trees found is a fairly efficient method for testing convergence. Typically, it would be nice to find the same best tree at least twice (if not three times), as opposed to simply performing some
fixed number of jumbles and hoping that at least one of them will be the optimum.
</text>
</comment>
</parameter>
<parameter>
<name>global_opp</name>
<prompt lang="en">Global rearrangements</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">defined $transition or $bootstrap or $jumble</code>
<code proglang="python">transition is not None or bootstrap or jumble</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " global " : ""</code>
<code proglang="python">( "" , " global ")[ value ]</code>
</format>
<argpos>11</argpos>
<comment>
<text lang="en">The G (global) option has been generalized to permit crossing any number of branches during tree rearrangements. In addition, it is possible to modify the extent of rearrangement explored during the sequential addition phase of tree building.</text>
<text lang="en">The G U (global and user tree) option combination instructs the program to find the best of the user trees, and then look for rearrangements that are better still.</text>
<text lang="en">If a rearrangement distance is specified, the input must contain a transition option.</text>
<text lang="en">The Global option can be used to force branch swapping on user trees, (combination of Global and User Tree(s) options).</text>
</comment>
</parameter>
<parameter>
<name>final_arrgt</name>
<prompt lang="en">Number of branches to cross in rearrangements of the completed tree</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">(defined $transition or $bootstrap or $jumble) and $global_opp</code>
<code proglang="python">(transition is not None or bootstrap or jumble) and global_opp</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? " $final_arrgt " : ""</code>
<code proglang="python">( "" , " %s " % str(final_arrgt))[ value is not None]</code>
</format>
<argpos>12</argpos>
</parameter>
<parameter>
<name>partial_arrgt</name>
<prompt lang="en">Number of branches to cross in testing rearrangements during the sequential addition phase of tree inference</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">(defined $transition or $bootstrap or $jumble) and $global_opp</code>
<code proglang="python">(transition is not None or bootstrap or jumble) and global_opp</code>
</precond>
<format>
<code proglang="perl">(defined $value) ? "$partial_arrgt " : ""</code>
<code proglang="python">( "" , " %s " % str(partial_arrgt))[ value is not None]</code>
</format>
<argpos>13</argpos>
</parameter>
<parameter ishidden="1">
<name>pipe_arrgt</name>
<prompt lang="en">Number of branches to cross in testing rearrangements during the sequential addition phase of tree inference</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">(defined $transition or $bootstrap or $jumble) and $global_opp</code>
<code proglang="python">(transition is not None or bootstrap or jumble) and global_opp</code>
</precond>
<format>
<code proglang="perl">" | "</code>
<code proglang="python">" | "</code>
</format>
<argpos>14</argpos>
</parameter>
<parameter>
<name>quickadd</name>
<prompt lang="en">Decreases the time in initially placing a new sequence in the growing tree (quickadd)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? "quickadd | " : ""</code>
<code proglang="python">( "" , " quickadd | " )[ value ]</code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">This option greatly decreases the time in initially placing a new sequence in the growing tree (but does not change the time required to subsequently test rearrangements). The overall time savings seems to be about 30%, based on a very limited number of test cases. Its downside, if any, is unknown. This will probably become default program behavior in the near future.</text>
<text lang="en">If the analysis is run with a global option of 'G 0 0', so that no rearrangements are permitted, the tree is build very approximately, but very quickly. This may be of greatest interest if the question is, 'Where does this one new sequence fit into this known tree?' The known tree is provided with the restart option, below.</text>
<text lang="en">PHYLIP DNAML does not include anything comparable to the quickadd option.</text>
</comment>
</parameter>
<parameter>
<name>outgroup</name>
<prompt lang="en">Use the specified sequence number as outgroup</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? "outgroup $value | " : ""</code>
<code proglang="python">( "" , "outgroup " + str(value) + " | " )[ value is not None ]</code>
</format>
<argpos>2</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>treeopt</name>
<prompt lang="en">User input Tree Options</prompt>
<precond>
<code proglang="perl">not $bootstrap</code>
<code proglang="python">not bootstrap</code>
</precond>
<comment>
<text lang="en">This options allows you to enter your own trees and instructs the program to evaluate them.</text>
</comment>
<parameters>
<parameter>
<name>user_tree</name>
<prompt lang="en">User tree - tree(s) file</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<format>
<code proglang="perl">(defined $value) ? "usertree $value |" : ""</code>
<code proglang="python">( "" , " usertree %s |" % str(value) )[ value is not None ]</code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">The trees must be in Newick format, and terminated with a semicolon. (The program also accepts a pseudo_newick format, which is a valid prolog fact.)</text>
<text lang="en">The tree reader in this program is more powerful than that in PHYLIP 3.3. In particular, material enclosed in square brackets, [ like this ], is ignored as comments; taxa names can be wrapped in single quotation marks to support the inclusion of characters that would otherwise end the name (i.e., '(', ')', ':', ';', '[', ']', ',' and ' '); names of internal nodes are properly ignored; and exponential notation (such as 1.0E-6) for branch lengths is supported.</text>
</comment>
</parameter>
<parameter>
<name>user_lengths</name>
<prompt lang="en">User trees to be read with branch lengths</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $bootstrap</code>
<code proglang="python">not bootstrap</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "userlengths |" : ""</code>
<code proglang="python">( "" , "userlengths |" )[ value ]</code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">Causes user trees to be read with branch lengths (and it is an error to omit any of them). Without the L option, branch lengths in user trees are not required, and are ignored if present.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>boot</name>
<prompt lang="en">Bootstrap</prompt>
<parameters>
<parameter issimple="1">
<name>bootstrap</name>
<prompt lang="en">Generates a re-sample of the input data (bootstrap)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " fastdnaml " : ""</code>
<code proglang="python">( "" , " fastdnaml " )[ value ]</code>
</format>
<argpos>1001</argpos>
<comment>
<text lang="en">Tree files will be summarized in one '.tree' file as well as output files in one '.out' file</text>
</comment>
</parameter>
<paragraph>
<name>bootopt</name>
<prompt lang="en">Bootstrap options</prompt>
<precond>
<code proglang="perl">$bootstrap</code>
<code proglang="python">bootstrap</code>
</precond>
<parameters>
<parameter issimple="1">
<name>nboots</name>
<prompt lang="en">Number of different bootstrap samples</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -boots $value" : ""</code>
<code proglang="python">( "" , " -boots " + str(value) )[ value is not None and value != vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">More than 1000 samples is not possible on this server</text>
</message>
<code proglang="perl">$value <= 1000</code>
<code proglang="python">value <= 1000</code>
</ctrl>
<argpos>1002</argpos>
</parameter>
<parameter issimple="1">
<name>bootstrap_seed</name>
<prompt lang="en">Random number seed for first bootstrap</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -seed $value" : ""</code>
<code proglang="python">( "" , " -seed " + str(value) )[ value is not None ]</code>
</format>
<argpos>1002</argpos>
<comment>
<text lang="en">Warning: For a given random number seed, the sample will always be the same.</text>
</comment>
</parameter>
<parameter>
<name>bootstrap_maxjumble</name>
<prompt lang="en">Maximum attempts at replicating inferred tree (max jumble)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$bootstrap</code>
<code proglang="python">bootstrap</code>
</precond>
<vdef>
<value>10</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -jumble $value" : ""</code>
<code proglang="python">( "" , " -jumble " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>1002</argpos>
</parameter>
<parameter ishidden="1">
<name>in_bootfile</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">" $infile.tmp"</code>
<code proglang="python">" %s.tmp" % str(infile)</code>
</format>
<argpos>1003</argpos>
</parameter>
</parameters>
</paragraph>
</parameters>
</paragraph>
<paragraph>
<name>output_opt</name>
<prompt lang="en">Output and Results Options</prompt>
<parameters>
<parameter>
<name>outfile</name>
<prompt lang="en">Output File</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $bootstrap</code>
<code proglang="python">not bootstrap</code>
</precond>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " > $outfile" : ""</code>
<code proglang="python">( "" , " > " + str(outfile) )[ value is not None ]</code>
</format>
<argpos>1010</argpos>
</parameter>
<parameter isstdout="1">
<name>outputfile</name>
<prompt lang="en">Output(s) file</prompt>
<type>
<datatype>
<class>Report</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $bootstrap and not defined $outfile</code>
<code proglang="python">not bootstrap and outfile is None</code>
</precond>
<filenames>
<code proglang="perl">"fastdnaml.out"</code>
<code proglang="python">"fastdnaml.out"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>outputfile_name</name>
<prompt lang="en">Output(s) file</prompt>
<type>
<datatype>
<class>Report</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $bootstrap and defined $outfile</code>
<code proglang="python">not bootstrap and outfile is not None</code>
</precond>
<filenames>
<code proglang="perl">"$outfile"</code>
<code proglang="python">str(outfile)</code>
</filenames>
</parameter>
<parameter>
<name>treefile</name>
<prompt lang="en">Save tree in treefile</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">not $bootstrap</code>
<code proglang="python">not bootstrap</code>
</precond>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($value) ? "" : "treefile | "</code>
<code proglang="python">( "treefile | ", "" )[ value ]</code>
</format>
<argpos>2</argpos>
</parameter>
<parameter>
<name>printdata</name>
<prompt lang="en">Print the input alignment at start of run (printdata)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? "printdata | " : ""</code>
<code proglang="python">( "" , "printdata | " )[ value ]</code>
</format>
<argpos>2</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>categopt</name>
<prompt lang="en">Categories and Weights Options</prompt>
<parameters>
<parameter>
<name>categories</name>
<prompt lang="en">Rate categories file (user-specified)</prompt>
<type>
<datatype>
<class>PhylipCategoriesRates</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? "categories $value |" : ""</code>
<code proglang="python">( "" , "categories "+ str(value) + " |" )[ value is not None ]</code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">
The data must have the format specified for PHYLIP dnaml 3.3. The first line must be the letter C, followed by the number of categories (a number in the range 1 through 35), and then a blank-separated list of the rates for each category. (The list can take more than one line; the program reads until it finds the specified number of rate values.) The next line should be the word Categories followed by one rate category character per sequence position. The categories 1 - 35 are
represented by the series 1, 2, 3, ..., 8, 9, A, B, C, ..., Y, Z. These latter data can be on one or more lines. For example:
</text>
<text lang="en">C 12 0.0625 0.125 0.25 0.5 1 2 4 8 16 32 64 128</text>
<text lang="en">Categories 5111136343678975AAA8949995566778888889AAAAAA9239898629AAAAA9</text>
<text lang="en">Category 'numbers' are ordered: 1, 2, 3, ..., 9, A, B, ..., Y, Z. Category zero (undefined rate) is permitted at sites with a zero in a user-supplied weighting mask.</text>
</comment>
</parameter>
<parameter>
<name>weights</name>
<prompt lang="en">Weights file (user-specified column weighting information)</prompt>
<type>
<datatype>
<class>PhylipWeight</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? "weights $value |" : ""</code>
<code proglang="python">( "" , "weights " + str(value) + " |" )[ value is not None ]</code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">example:</text>
<text lang="en">Weights 111111111111001100000100011111100000000000000110000110000000</text>
<text lang="en">In case of bootstrap, only positions that have nonzero weights are used in computing the bootstrap sample.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<parameter isout="1">
<name>treefiles</name>
<prompt>Tree file</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<precond>
<code proglang="perl">not $bootstrap</code>
<code proglang="python">not bootstrap</code>
</precond>
<filenames>
<code proglang="perl">"_treefile.[0-9]*"</code>
<code proglang="python">"_treefile.[0-9]*"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>bootstrap_report</name>
<prompt>Bootstrap output report</prompt>
<type>
<datatype>
<class>Report</class>
</datatype>
</type>
<precond>
<code proglang="perl">$bootstrap</code>
<code proglang="python">bootstrap</code>
</precond>
<filenames>
<code proglang="perl">"$infile.tmp.out"</code>
<code proglang="python">"%s.tmp.out" % str(infile)</code>
</filenames>
</parameter>
<parameter isout="1">
<name>bootstrap_tree</name>
<prompt>Bootstrap tree file</prompt>
<type>
<datatype>
<class>Tree</class>
</datatype>
<dataFormat>NEWICK</dataFormat>
</type>
<precond>
<code proglang="perl">$bootstrap</code>
<code proglang="python">bootstrap</code>
</precond>
<filenames>
<code proglang="perl">"$infile.tmp.tree"</code>
<code proglang="python">"%s.tmp.tree" % str(infile)</code>
</filenames>
</parameter>
<parameter isout="1">
<name>bootstrap_aln</name>
<prompt>Bootstrap alignment file</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
</type>
<precond>
<code proglang="perl">$bootstrap</code>
<code proglang="python">bootstrap</code>
</precond>
<filenames>
<code proglang="perl">"$infile.tmp"</code>
<code proglang="python">"%s.tmp" % str(infile)</code>
</filenames>
</parameter>
</parameters>
</program>
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