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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>bambe</name>
    <version>4.01</version>
    <doc>
      <title>BAMBE</title>
      <description>
        <text lang="en">Bayesian Analysis in Molecular Biology and Evolution</text>
      </description>
      <authors>Simon, Larget</authors>
      <reference>Larget, B. and D. Simon (1999). Markov chain Monte
	Carlo algorithms for the Bayesian analysis of phylogenetic
	trees. Molecular Biology and Evolution 16:750-759.</reference>
      <reference>Simon, D. and B. Larget. 1998. Bayesian analysis in
	molecular biology and evolution (BAMBE), version 1.01
	beta. Department of Mathematics and Computer Science, Duquesne
	University.</reference>
      <homepagelink>http://www.stat.wisc.edu/~larget/</homepagelink>
      <sourcelink>http://www.stat.wisc.edu/~larget/</sourcelink>
    </doc>
    <category>phylogeny:bayesian</category>
  </head>
  <parameters>
    <parameter iscommand="1" ishidden="1">
      <name>bambe</name>
      <type>
        <datatype>
          <class>String</class>
        </datatype>
      </type>
      <format>
        <code proglang="perl">"bambe &lt;bambe.params"</code>
        <code proglang="python">"bambe &lt;bambe.params"</code>
      </format>
      <argpos>0</argpos>
    </parameter>
    <parameter ismandatory="1" issimple="1">
      <name>data_file</name>
      <prompt lang="en">Alignment file (data-file)</prompt>
      <type>
        <biotype>DNA</biotype>
        <datatype>
          <class>Alignment</class>
        </datatype>
        <dataFormat>CLUSTAL</dataFormat>
      </type>
      <format>
        <code proglang="perl">"data-file=$value\\n"</code>
        <code proglang="python">"data-file="+str(value)+"\n"</code>
      </format>
      <argpos>6</argpos>
      <paramfile>bambe.params</paramfile>
    </parameter>
    <paragraph>
      <name>run_options</name>
      <prompt lang="en">Run characteristics</prompt>
      <argpos>1</argpos>
      <parameters>
        <parameter>
          <name>seed</name>
          <prompt lang="en">Seed for random number generator (seed)</prompt>
          <type>
            <datatype>
              <class>Integer</class>
            </datatype>
          </type>
          <vdef>
            <value>194024933</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value != $vdef) ? "seed=$value\\n" : ""</code>
            <code proglang="python">("", "seed="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>cycles</name>
          <prompt lang="en">Number of cycles to run the main algorithm (cycles)</prompt>
          <type>
            <datatype>
              <class>Integer</class>
            </datatype>
          </type>
          <vdef>
            <value>1000</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value != $vdef) ?"cycles=$value\\n" : ""</code>
            <code proglang="python">("", "cycles="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>window_interval</name>
          <prompt lang="en">Number of cycles between printing trees to output (window-interval)</prompt>
          <type>
            <datatype>
              <class>Integer</class>
            </datatype>
          </type>
          <vdef>
            <value>200</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value != $vdef) ? "window-interval=$value\\n" : ""</code>
            <code proglang="python">("", "window-interval="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <comment>
            <text lang="en">Also used for updating the window size during burn-in.</text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>main_algorithm</name>
          <prompt lang="en">Algorithm to run during production cycles (main-algorithm)</prompt>
          <type>
            <datatype>
              <class>Choice</class>
            </datatype>
          </type>
          <vdef>
            <value>local</value>
          </vdef>
          <vlist>
            <velem>
              <value>global</value>
              <label>Global</label>
            </velem>
            <velem>
              <value>local</value>
              <label>Local</label>
            </velem>
          </vlist>
          <format>
            <code proglang="perl">(defined $value and $value ne $vdef) ? "main-algorithm=$value\\n" : ""</code>
            <code proglang="python">("", "main-algorithm="+str(value)+"\n")[value is not None and value != vdef]</code>
          </format>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>burn</name>
          <prompt lang="en">Number of cycles to run the burn algorithm (burn)</prompt>
          <type>
            <datatype>
              <class>Integer</class>
            </datatype>
          </type>
          <vdef>
            <value>1000</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value != $vdef) ? "burn=$value\\n" : ""</code>
            <code proglang="python">("", "burn="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <comment>
            <text lang="en">Parameter values are not updated during burn. User should discard these cycles and the initial cycles of the main algorithm before inference.</text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>burn_algorithm</name>
          <prompt lang="en">Algorithm to run during burn (burn-algorithm)</prompt>
          <type>
            <datatype>
              <class>Choice</class>
            </datatype>
          </type>
          <vdef>
            <value>global</value>
          </vdef>
          <vlist>
            <velem>
              <value>global</value>
              <label>Global</label>
            </velem>
            <velem>
              <value>local</value>
              <label>Local</label>
            </velem>
          </vlist>
          <format>
            <code proglang="perl">(defined $value and $value ne $vdef) ? "burn-algorithm=$value\\n" : ""</code>
            <code proglang="python">("","burn-algorithm="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>use_beta</name>
          <prompt lang="en">Use scaled beta distribution modification of the local algorithm (use-beta)</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$main_algorithm eq "local" or $burn_algorithm eq "local"</code>
            <code proglang="python">main_algorithm == "local" or burn_algorithm == "local"</code>
          </precond>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="perl">($value) ? "use-beta=true\\n" : ""</code>
            <code proglang="python">("", "use-beta=true\n")[ value ]</code>
          </format>
          <paramfile>bambe.params</paramfile>
        </parameter>
      </parameters>
    </paragraph>
    <paragraph>
      <name>model_options</name>
      <prompt lang="en">Model specification</prompt>
      <argpos>2</argpos>
      <parameters>
        <parameter>
          <name>molecular_clock</name>
          <prompt lang="en">Use a molecular clock (molecular-clock)</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>1</value>
          </vdef>
          <format>
            <code proglang="perl">($value) ? "" :"molecular-clock=false\\n"</code>
            <code proglang="python">("molecular-clock=false\n", "")[ value ]</code>
          </format>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>likelihood_model</name>
          <prompt lang="en">Likelihood model (likelihood-model)</prompt>
          <type>
            <datatype>
              <class>Choice</class>
            </datatype>
          </type>
          <vdef>
            <value>HKY85</value>
          </vdef>
          <vlist>
            <velem>
              <value>HKY85</value>
              <label>Hasegawa, Kishino, Yano (HKY85)</label>
            </velem>
            <velem>
              <value>F84</value>
              <label>Felsenstein's PHYLIP (F84)</label>
            </velem>
            <velem>
              <value>TN93</value>
              <label>Tamura-Nei (TN93)</label>
            </velem>
            <velem>
              <value>GREV</value>
              <label>Hayley (GREV)</label>
            </velem>
          </vlist>
          <format>
            <code proglang="perl">(defined $value and $value ne $vdef) ? "likelihood-model=$value\\n" : ""</code>
            <code proglang="python">("", "likelihood-model="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>category_list</name>
          <prompt lang="en">A valid category list (category-list)</prompt>
          <type>
            <datatype>
              <class>String</class>
            </datatype>
          </type>
          <format>
            <code proglang="perl">(defined $value) ? "category-list=$value\\n" :""</code>
            <code proglang="python">("", "category-list="+str(value)+"\n" )[value is not None]</code>
          </format>
          <comment>
            <text lang="en">Each category has its own set of parameters. Each category is denoted by a positive integer between 1 and 10. A comma-separated list gives the categories of the sites in order, e.g., 1,2,3,1,3 means that the first site is in category 1, the second in 2, the third in 3, the fourth in 1, and the fifth site is in category 3.</text>
            <text lang="en">A repeat count is indicated by a caret (^). For example, 1^20,2^5,3^2 means that the first twenty sites are in category 1, the next five sites are in 2, and the next two sites are in category 3.</text>
            <text lang="en">Parentheses may be used to group sites together with a common repeat count, i.e., (1,2)^5 is the same as 1,2,1,2,1,2,1,2,1,2. Repeat counts may be nested, e.g., (1^3,2)^2 is the same as 1,1,1,2,1,1,1,2.</text>
            <text lang="en">Repetition to the end of the list of sites is indicated by an asterisk (*). For example, 1^5,2* means that the first five sites are in category 1, and all the remaining sites are in category 2. Parentheses may also be used in conjunction with the asterisk, e.g., (1,2)* is the same as 1,2,1,2,1,2,.... The category list may contain at most one asterisk and it must be associated with the last category or group in the list. In other words, an asterisk may appear only at the end of the list.</text>
            <text lang="en">Examples</text>
            <text lang="en">1* - all sites are the same category. (default)</text>
            <text lang="en">(1,2,3)* - all sites are partitioned by codon position.</text>
            <text lang="en">1^99,2^50,3^9 - the sites are divided over three genes. Each gene has its own set of parameters used by all sites in that gene. The first gene is composed of the first ninety-nine sites, the next by the next fifty sites, and the last by nine sites.</text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>single_kappa</name>
          <prompt lang="en">Single kappa (single-kappa)</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="perl">($value) ? "single-kappa=true\\n" : ""</code>
            <code proglang="python">("", "single-kappa=true\n")[ value ]</code>
          </format>
          <comment>
            <text lang="en">If true, the same kappa parameter is used for all site categories. If false, there are different values for different site categories. It has no effect if there is only one rate category.</text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>initial_kappa</name>
          <prompt lang="en">Comma separated list of positive kappa values for each site category (initial-kappa)</prompt>
          <type>
            <datatype>
              <class>String</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$likelihood_model eq "HKY85" or $likelihood_model eq "F84"</code>
            <code proglang="python">likelihood_model=="HKY85" or likelihood_model=="F84"</code>
          </precond>
          <vdef>
            <value>7.5,2.5,10.75</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value ne $vdef) ? "initial-kappa=$value\\n" : ""</code>
            <code proglang="python">("", "initial-kappa="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <comment>
            <text lang="en">If single-kappa is true, a warning is given if more than one value is specified. The first value will be used. If single-kappa is false, a value must be specified for each category in use.</text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>initial_theta</name>
          <prompt lang="en">Comma separated list of positive theta values for each site category (initial-theta)</prompt>
          <type>
            <datatype>
              <class>String</class>
            </datatype>
          </type>
          <vdef>
            <value>1.4,1.0,8.3</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value ne $vdef) ? "initial-theta=$value\\n" : ""</code>
            <code proglang="python">("", "initial-theta="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <comment>
            <text lang="en">The weighted average of these values should be 1, with weights given by the proportion of sites in each site category. (Renormalization is automatic and a warning given if the condition fails.) If there are an equal number of sites in each category, for example, the numbers should average to 1.</text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>estimate_pi</name>
          <prompt lang="en">Use empirical relative frequencies (estimate-pi)</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>1</value>
          </vdef>
          <format>
            <code proglang="perl">($value) ? "" : "estimate-pi=false\\n"</code>
            <code proglang="python">("estimate-pi=false\n","")[ value ]</code>
          </format>
          <comment>
            <text lang="en">If true, the initial stationary probabilities for each base in each category are estimated by the relative frequencies with which they appear in the data.</text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>initial_pia</name>
          <prompt lang="en">Comma separated list of initial pi value of base A (initial-pia)</prompt>
          <type>
            <datatype>
              <class>String</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">not $estimate_pi</code>
            <code proglang="python">not estimate_pi</code>
          </precond>
          <vdef>
            <value>0.25,0.25,0.25</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value ne $vdef) ? "initial-pia=$value\\n" : ""</code>
            <code proglang="python">("", "initial-pia="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
        </parameter>
        <parameter>
          <name>initial_pig</name>
          <prompt lang="en">Comma separated list of initial pi value of base G (initial-pig)</prompt>
          <type>
            <datatype>
              <class>String</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">not $estimate_pi</code>
            <code proglang="python">not estimate_pi</code>
          </precond>
          <vdef>
            <value>0.25,0.25,0.25</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value ne $vdef) ? "initial-pig=$value\\n" : ""</code>
            <code proglang="python">("", "initial-pig="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
        </parameter>
        <parameter>
          <name>initial_pic</name>
          <prompt lang="en">Comma separated list of initial pi value of base C (initial-pic)</prompt>
          <type>
            <datatype>
              <class>String</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">not $estimate_pi</code>
            <code proglang="python">not estimate_pi</code>
          </precond>
          <vdef>
            <value>0.25,0.25,0.25</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value ne $vdef) ? "initial-pic=$value\\n" : ""</code>
            <code proglang="python">("", "initial-pic="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
        </parameter>
        <parameter>
          <name>initial_pit</name>
          <prompt lang="en">Comma separated list of initial pi value of base T (initial-pit)</prompt>
          <type>
            <datatype>
              <class>String</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">not $estimate_pi</code>
            <code proglang="python">not estimate_pi</code>
          </precond>
          <vdef>
            <value>0.25,0.25,0.25</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value ne $vdef) ? "initial-pit=$value\\n" : ""</code>
            <code proglang="python">("","initial-pit="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
        </parameter>
        <parameter>
          <name>initial_ttp</name>
          <prompt lang="en">Comma separated list of positive transition/transversion parameter values (TN93 model) (initial-ttp)</prompt>
          <type>
            <datatype>
              <class>String</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$likelihood_model eq "TN93"</code>
            <code proglang="python">likelihood_model  == "TN93"</code>
          </precond>
          <vdef>
            <value>1.0,1.0,1.0</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value ne $vdef) ? "initial-ttp=$value\\n" : ""</code>
            <code proglang="python">("", "initial-ttp="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <comment>
            <text lang="en">This is used only with TN93. There must be a value specified for each site-category used if TN93 is the chosen model.</text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>initial_gamma</name>
          <prompt lang="en">Comma separated list of positive gamma values (TN93 model) (initial-gamma)</prompt>
          <type>
            <datatype>
              <class>String</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$likelihood_model eq "TN93"</code>
            <code proglang="python">likelihood_model  == "TN93"</code>
          </precond>
          <vdef>
            <value>1.0,1.0,1.0</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value ne $vdef) ? "initial-gamma=$value\\n" : ""</code>
            <code proglang="python">("", "initial-gamma="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <comment>
            <text lang="en">This is used only with TN93. There must be a value specified for each site-category used if TN93 is the chosen model.</text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>initial_Rac</name>
          <prompt lang="en">Comma separated list of positive r values for AC bases(GREV model) (initial-rac)</prompt>
          <type>
            <datatype>
              <class>String</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$likelihood_model eq "GREV"</code>
            <code proglang="python">likelihood_model  == "GREV"</code>
          </precond>
          <vdef>
            <value>1.0,1.0,1.0</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value ne $vdef) ? "initial-rac=$value\\n" : ""</code>
            <code proglang="python">("", "initial-rac="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <comment>
            <text lang="en">This is used only with GREV model. </text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>initial_Rag</name>
          <prompt lang="en">Comma separated list of positive r values for AG  (GREV model) (initial-rag)</prompt>
          <type>
            <datatype>
              <class>String</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$likelihood_model eq "GREV"</code>
            <code proglang="python">likelihood_model  == "GREV"</code>
          </precond>
          <vdef>
            <value>1.0,1.0,1.0</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value ne $vdef) ? "initial-rag=$value\\n" : ""</code>
            <code proglang="python">("", "initial-rag="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <comment>
            <text lang="en">This is used only with GREV model. </text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>initial_Rat</name>
          <prompt lang="en">Comma separated list of positive r values for AT (GREV model) (initial-rat)</prompt>
          <type>
            <datatype>
              <class>String</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$likelihood_model eq "GREV"</code>
            <code proglang="python">likelihood_model  == "GREV"</code>
          </precond>
          <vdef>
            <value>1.0,1.0,1.0</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value ne $vdef) ? "initial-rat=$value\\n" : ""</code>
            <code proglang="python">("", "initial-rat="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <comment>
            <text lang="en">This is used only with GREV model. </text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>initial_Rcg</name>
          <prompt lang="en">Comma separated list of positive r values for CG (GREV model) (initial-rcg)</prompt>
          <type>
            <datatype>
              <class>String</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$likelihood_model eq "GREV"</code>
            <code proglang="python">likelihood_model  == "GREV"</code>
          </precond>
          <vdef>
            <value>1.0,1.0,1.0</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value ne $vdef) ? "initial-rcg=$value\\n" : ""</code>
            <code proglang="python">("", "initial-rcg="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <comment>
            <text lang="en">This is used only with GREV model. </text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>initial_Rct</name>
          <prompt lang="en">Comma separated list of positive r values for CT (GREV model) (initial-rct)</prompt>
          <type>
            <datatype>
              <class>String</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$likelihood_model eq "GREV"</code>
            <code proglang="python">likelihood_model  == "GREV"</code>
          </precond>
          <vdef>
            <value>1.0,1.0,1.0</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value ne $vdef) ? "initial-rct=$value\\n" : ""</code>
            <code proglang="python">("", "initial-rct="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <comment>
            <text lang="en">This is used only with GREV model. </text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>initial_Rgt</name>
          <prompt lang="en">Comma separated list of positive r values for GT  (GREV model) (initial-rct)</prompt>
          <type>
            <datatype>
              <class>String</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$likelihood_model eq "GREV"</code>
            <code proglang="python">likelihood_model  == "GREV"</code>
          </precond>
          <vdef>
            <value>1.0,1.0,1.0</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value ne $vdef) ? "initial-rgt=$value\\n" : ""</code>
            <code proglang="python">("", "initial-rgt="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <comment>
            <text lang="en">This is used only with GREV model. </text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
      </parameters>
    </paragraph>
    <paragraph>
      <name>param_update</name>
      <prompt lang="en">Parameter updating</prompt>
      <argpos>4</argpos>
      <parameters>
        <parameter>
          <name>parameter_update_interval</name>
          <prompt lang="en">Parameter update interval (parameter-update-interval)</prompt>
          <type>
            <datatype>
              <class>Integer</class>
            </datatype>
          </type>
          <vdef>
            <value>1</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value != $vdef) ? "parameter-update-interval=$value\\n" : ""</code>
            <code proglang="python">("", "parameter-update-interval="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <comment>
            <text lang="en">During the main algorithm, any 'on' parameters are updated at each cycle divisible by this value. Use zero for no parameter updating.</text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>update_kappa</name>
          <prompt lang="en">Update kappa value (update-kappa)</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$likelihood_model eq "HKY85" or $likelihood_model eq "F84"</code>
            <code proglang="python">likelihood_model=="HKY85" or likelihood_model=="F84"</code>
          </precond>
          <vdef>
            <value>1</value>
          </vdef>
          <format>
            <code proglang="perl">($value) ? "" : "update-kappa=false\\n"</code>
            <code proglang="python">("update-kappa=false\n", "")[ value ]</code>
          </format>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>update_theta</name>
          <prompt lang="en">Update theta value (update-theta)</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>1</value>
          </vdef>
          <format>
            <code proglang="perl">($value) ? "" : "update-theta=false\\n"</code>
            <code proglang="python">("update-theta=false\n", "")[ value ]</code>
          </format>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>update_pi</name>
          <prompt lang="en">Update pi value (update-pi)</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>1</value>
          </vdef>
          <format>
            <code proglang="perl">($value) ? "" : "update-pi=false\\n"</code>
            <code proglang="python">("update-pi=false\n", "")[ value ]</code>
          </format>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>update_ttp</name>
          <prompt lang="en">Update ttp value (TN93 model) (update-ttp)</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$likelihood_model eq "TN93"</code>
            <code proglang="python">likelihood_model == "TN93"</code>
          </precond>
          <vdef>
            <value>1</value>
          </vdef>
          <format>
            <code proglang="perl">($value) ? "" : "update-ttp=false\\n"</code>
            <code proglang="python">("update-ttp=false\n", "")[ value ]</code>
          </format>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>update_gamma</name>
          <prompt lang="en">Update gamma value for (TN93 model) (update-gamma)</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$likelihood_model eq "TN93"</code>
            <code proglang="python">likelihood_model == "TN93"</code>
          </precond>
          <vdef>
            <value>1</value>
          </vdef>
          <format>
            <code proglang="perl">($value) ? "" : "update-gamma=false\\n"</code>
            <code proglang="python">("update-gamma=false\n", "")[ value ]</code>
          </format>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>update_grev</name>
          <prompt lang="en">Update grev (GREV model) (update-grev)</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$likelihood_model eq "GREV"</code>
            <code proglang="python">likelihood_model == "GREV"</code>
          </precond>
          <vdef>
            <value>1</value>
          </vdef>
          <format>
            <code proglang="perl">($value) ? "" : "update-grev=false\\n"</code>
            <code proglang="python">("update-grev=false\n", "")[ value ]</code>
          </format>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>update_invariant_prob</name>
          <prompt lang="en">Update invariant probability (update-invariant-prob)</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="perl">($value) ? "update-invariant-prob=true\\n" : ""</code>
            <code proglang="python">("", "update-invariant-prob=true\n")[ value ]</code>
          </format>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>local_tune</name>
          <prompt lang="en">Stretch parameter for local (local-tune)</prompt>
          <type>
            <datatype>
              <class>Float</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$burn_algorithm eq "local" or $main_algorithm eq "local"</code>
            <code proglang="python">burn_algorithm == "local" or main_algorithm == "local"</code>
          </precond>
          <vdef>
            <value>0.19</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value != $vdef) ? "local-tune=$value\\n" : ""</code>
            <code proglang="python">("", "local-tune="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <comment>
            <text lang="en">This tuning parameter is only used with the local algorithm. It modulates the size of a maximal stretch. The smaller the value, the greater the tree acceptance rate will be.</text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>theta_tune</name>
          <prompt lang="en">Dirichlet parameter for theta update (theta-tune)</prompt>
          <type>
            <datatype>
              <class>Float</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$parameter_update_interval != 0 and $update_theta</code>
            <code proglang="python">parameter_update_interval != 0 and update_theta</code>
          </precond>
          <vdef>
            <value>2000.0</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value != $vdef) ? "theta-tune=$value\\n" : ""</code>
            <code proglang="python">("","theta-tune="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <comment>
            <text lang="en">Tuning parameter used during update of theta value(s). The larger its value, the more likely proposals are to be accepted.</text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>pi_tune</name>
          <prompt lang="en">Dirichlet parameter for pi update (pi-tune)</prompt>
          <type>
            <datatype>
              <class>Float</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$parameter_update_interval != 0 and $update_pi</code>
            <code proglang="python">parameter_update_interval != 0 and update_pi</code>
          </precond>
          <vdef>
            <value>2000.0</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value != $vdef) ? "pi-tune=$value\\n" : ""</code>
            <code proglang="python">("", "pi-tune="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <comment>
            <text lang="en">Tuning parameter used during update of pi values. The larger its value, the more likely proposals are to be accepted.</text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>kappa_tune</name>
          <prompt lang="en">Halft the size of the window for uniform updates of kappa (kappa-tune)</prompt>
          <type>
            <datatype>
              <class>Float</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$parameter_update_interval != 0 and $update_kappa and ($likelihood_model eq "HKY85" or $likelihood_model eq "F84")</code>
            <code proglang="python">parameter_update_interval != 0 and update_kappa and (likelihood_model == "HKY85" or likelihood_model == "F84")</code>
          </precond>
          <vdef>
            <value>0.2</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value != $vdef) ? "kappa-tune=$value\\n" : ""</code>
            <code proglang="python">("","kappa-tune="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <comment>
            <text lang="en">This tuning parameter is only used when 'parameter-update-interval' is positive and 'update-kappa' is true. The smaller its value, the greater the parameter acceptance rate will be.</text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>ttp_tune</name>
          <prompt lang="en">Halft window width for ttp update (TN93 model) (ttp-tune)</prompt>
          <type>
            <datatype>
              <class>Float</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$parameter_update_interval != 0 and $update_ttp and $likelihood_model eq "TN93"</code>
            <code proglang="python">parameter_update_interval != 0 and update_ttp and likelihood_model == "TN93"</code>
          </precond>
          <vdef>
            <value>0.1</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value != $vdef) ? "ttp-tune=$value\\n" : ""</code>
            <code proglang="python">("","ttp-tune="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <comment>
            <text lang="en">This tuning parameter is only used when 'parameter-update-interval' is positive and 'update-ttp' is true. The smaller its value, the greater the parameter acceptance rate will be.</text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>gamma_tune</name>
          <prompt lang="en">Half window width for gamma update (TN93 model) (gamma-tune)</prompt>
          <type>
            <datatype>
              <class>Float</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$parameter_update_interval != 0 and $update_gamma and $likelihood_model eq "TN93"</code>
            <code proglang="python">parameter_update_interval != 0 and update_gamma and likelihood_model == "TN93"</code>
          </precond>
          <vdef>
            <value>0.1</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value != $vdef) ? "gamma-tune=$value\\n" : ""</code>
            <code proglang="python">("","gamma-tune="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <comment>
            <text lang="en">This tuning parameter is only used when 'parameter-update-interval' is positive and 'update-gamma' is true. The smaller its value, the greater the parameter acceptance rate will be.</text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>grev_tune</name>
          <prompt lang="en">Halft window width for grev update (grev-tune)</prompt>
          <type>
            <datatype>
              <class>Float</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$parameter_update_interval != 0 and $update_grev and $likelihood_model eq "GREV"</code>
            <code proglang="python">parameter_update_interval != 0 and update_grev and likelihood_model=="GREV"</code>
          </precond>
          <vdef>
            <value>2000</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value != $vdef) ? "grev-tune=$value\\n" : ""</code>
            <code proglang="python">("","grev-tune="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>beta_tune</name>
          <prompt lang="en">Beta parameter for local update (beta-tune)</prompt>
          <type>
            <datatype>
              <class>Float</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$use_beta</code>
            <code proglang="python">use_beta</code>
          </precond>
          <vdef>
            <value>10.0</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value != $vdef) ? "beta-tune=$value\\n" : ""</code>
            <code proglang="python">("","beta-tune="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>invariant_prob_tune</name>
          <prompt lang="en">Halft window width for invariant probability update (invariant-prob-tune)</prompt>
          <type>
            <datatype>
              <class>Float</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$parameter_update_interval != 0 and $update_invariant_prob</code>
            <code proglang="python">parameter_update_interval != 0 and update_invariant_prob</code>
          </precond>
          <vdef>
            <value>2000</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value != $vdef) ? "invariant-prob-tune=$value\\n" : ""</code>
            <code proglang="python">("","invariant-prob-tune="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <paramfile>bambe.params</paramfile>
        </parameter>
      </parameters>
    </paragraph>
    <paragraph>
      <name>output_options</name>
      <prompt lang="en">Output options</prompt>
      <argpos>2</argpos>
      <parameters>
        <parameter>
          <name>sample_interval</name>
          <prompt lang="en">Sample interval (sample-interval)</prompt>
          <type>
            <datatype>
              <class>Integer</class>
            </datatype>
          </type>
          <vdef>
            <value>200</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value != $vdef) ? "sample-interval=$value\\n" : ""</code>
            <code proglang="python">("","sample-interval="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <comment>
            <text lang="en">During burn and main algorithms, the tree topology, log likelihoods, and parameters are written to files at each cycle divisible by this value.</text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>newick_format</name>
          <prompt lang="en">Newick format of tree file (newick-format)</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>1</value>
          </vdef>
          <format>
            <code proglang="perl">($value) ? "newick-format=false\\n" : ""</code>
            <code proglang="python">("newick-format=false\n", "")[ value ]</code>
          </format>
          <comment>
            <text lang="en">Indicates the format of the tree to read (if not random) and the format of the tree to print after the run.</text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
      </parameters>
    </paragraph>
    <parameter isout="1">
      <name>results_files</name>
      <prompt>Results files</prompt>
      <type>
        <datatype>
          <class>Text</class>
        </datatype>
      </type>
      <filenames>
        <code proglang="perl">"bambe_results.lpd" and  "bambe_results.par" and  "bambe_results.out"</code>
        <code proglang="python">"bambe_results.lpd"</code>
        <code proglang="python">"bambe_results.par"</code>
        <code proglang="python">"bambe_results.out"</code>
      </filenames>
    </parameter>
    <parameter isout="1">
      <name>result_tree</name>
      <prompt>Tree file</prompt>
      <type>
        <datatype>
          <class>Tree</class>
        </datatype>
        <dataFormat>
          <test param="newick_format" eq="1">NEWICK</test>
          <test param="newick_format" eq="0">BAMBE</test>
        </dataFormat>
      </type>
      <filenames>
        <code proglang="perl">"bambe_results.tre"</code>
        <code proglang="python">"bambe_results.tre"</code>
      </filenames>
    </parameter>
    <parameter isout="1">
      <name>top_file</name>
      <prompt>Topology file</prompt>
      <type>
        <datatype>
          <class>Text</class>
        </datatype>
      </type>
      <filenames>
        <code proglang="perl">"bambe_results.top"</code>
        <code proglang="python">"bambe_results.top"</code>
      </filenames>
    </parameter>
    <parameter ishidden="1">
      <name>file_root</name>
      <type>
        <datatype>
          <class>String</class>
        </datatype>
      </type>
      <format>
        <code proglang="perl">"file-root=bambe_results\\n"</code>
        <code proglang="python">"file-root=bambe_results\n"</code>
      </format>
      <argpos>6</argpos>
      <paramfile>bambe.params</paramfile>
    </parameter>
    <paragraph>
      <name>input_options</name>
      <prompt lang="en">Input options</prompt>
      <argpos>7</argpos>
      <parameters>
        <parameter>
          <name>outgroup</name>
          <prompt lang="en">Number of the outgroup (outgroup)</prompt>
          <type>
            <datatype>
              <class>Integer</class>
            </datatype>
          </type>
          <precond>
            <code proglang="perl">$molecular_clock</code>
            <code proglang="python">molecular_clock</code>
          </precond>
          <vdef>
            <value>1</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value != $vdef) ? "outgroup=$value\\n" : ""</code>
            <code proglang="python">("", "outgroup="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <comment>
            <text lang="en">This is ignored if a molecular clock is assumed. In the absence of a clock, trees and tree topologies are printed with the outgroup emerging directly from the root.</text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>tree_file</name>
          <prompt lang="en">Tree file (tree-file)</prompt>
          <type>
            <datatype>
              <class>Tree</class>
            </datatype>
            <dataFormat>
            	<test param="initial_tree_type" eq="newick">NEWICK</test>
            	<test param="initial_tree_type" eq="bambe">BAMBE</test>
            </dataFormat>
          </type>
          <precond>
            <code proglang="perl">$initial_tree_type eq "bambe" or $initial_tree_type eq "newick"</code>
            <code proglang="python">initial_tree_type=="bambe" or initial_tree_type=="newick"</code>
          </precond>
          <format>
            <code proglang="perl">(defined $value) ? "tree-file=$value\\n" : ""</code>
            <code proglang="python">("", "tree-file="+str(value)+"\n")[value is not None]</code>
          </format>
          <comment>
            <text lang="en">If no tree file is given, the program generates a random tree from a flat distribution where each labeled history is equally likely.</text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>initial_tree_type</name>
          <prompt lang="en">Initial tree type (initial-tree-type)</prompt>
          <type>
            <datatype>
              <class>Choice</class>
            </datatype>
          </type>
          <vdef>
            <value>random</value>
          </vdef>
          <vlist>
            <velem>
              <value>random</value>
              <label>Random</label>
            </velem>
            <velem>
              <value>upgma</value>
              <label>UPGMA</label>
            </velem>
            <velem>
              <value>neighbor-joining</value>
              <label>Neighbor-Joining</label>
            </velem>
            <velem>
              <value>newick</value>
              <label>Newick</label>
            </velem>
            <velem>
              <value>bambe</value>
              <label>Bambe</label>
            </velem>
          </vlist>
          <format>
            <code proglang="perl">(defined $value and $value ne $vdef) ? "initial-tree-type=$value\\n" : ""</code>
            <code proglang="python">("", "initial-tree-type="+str(value)+"\n")[value is not None and value != vdef]</code>
          </format>
          <comment>
            <text lang="en">. random select a tree from the prior</text>
            <text lang="en">. upgma sets the initial clock tree to the UPGMA tree using maximum likelihood distances with the specified model and initial parameter values.</text>
            <text lang="en">. neighbor-joining sets the initial nonclock tree to the neigbor joining tree using maximum likelihood distances with the specified model and initial parameter values.</text>
            <text lang="en">. newick reads in an initial tree in Newick format from a file.</text>
            <text lang="en">. bambe reads in an initial tree in BAMBE format from a file.</text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>print_all_trees</name>
          <prompt lang="en">Print all trees?(print-all-trees)</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>1</value>
          </vdef>
          <format>
            <code proglang="perl">($value) ? "" : "print-all-trees=false\\n"</code>
            <code proglang="python">("print-all-trees=false\n", "")[value ]</code>
          </format>
          <paramfile>bambe.params</paramfile>
        </parameter>
        <parameter>
          <name>max_initial_tree_height</name>
          <prompt lang="en">Initial tree height used to generate an initial random tree (max-initial-tree-height)</prompt>
          <type>
            <datatype>
              <class>Float</class>
            </datatype>
          </type>
          <vdef>
            <value>0.1</value>
          </vdef>
          <format>
            <code proglang="perl">(defined $value and $value != $vdef) ? "max-initial-tree-height=$value\\n" : ""</code>
            <code proglang="python">("", "max-initial-tree-height="+str(value)+"\n")[value is not None and value!=vdef]</code>
          </format>
          <comment>
            <text lang="en">This parameter is only used to generate an initial random tree.</text>
          </comment>
          <paramfile>bambe.params</paramfile>
        </parameter>
      </parameters>
    </paragraph>
  </parameters>
</program>