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Uploaded Tool Config file
author malex
date Fri, 02 Dec 2011 17:06:40 -0500
parents
children 9ce35d2d9937
files garli.xml
diffstat 1 files changed, 868 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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+<tool id="Garli" name="Garli" version="2.0" force_history_refresh="True">
+  <description> phylogenetic inference using the maximum-likelihood</description>
+## The command is a Cheetah template which allows some Python based syntax.
+## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
+## Arguments to the wrapper beyond the config file are just for Galaxy's benefit - all filenames are hardcoded
+<command interpreter="python">garli_wrapper.py $garli_conf $best_all_tre $best_tre $log00_log $screen_log </command>
+  <inputs>
+    <param name="datafname" format="nexus" type="data" label="Nexus formated sequence file" force_select="true"/>
+    <conditional name="choose_search_type">
+        <param name="search_type" type="select" label="Analysis Type">
+            <option value="mlsearch" selected="true">ML Search</option>
+            <option value="bootstrap">Bootstrap</option>
+        </param>
+            <when value="mlsearch">
+                <param name="searchreps" type="integer" size="4" value="1" label="Number of replicates">
+                    <validator type="in_range" message="(1-infinity)" min="1" max="inf"/>
+                </param>
+                <param name="bootstrapreps" type="hidden" value="0" />
+                <param name="resampleproportion" type="float"
+                    value="1.0" label="Relative size of resample data
+                    matrix (0.1-10.0)">
+                    <validator type="in_range" message="(0.1-10.0)" min="0.1" max="10.0"/>
+                </param>
+            </when>
+            <when value="bootstrap">
+                <param name="searchreps" type="hidden" value="0" />
+                <param name="bootstrapreps" type="integer" size="4"
+                    value="1" label="Number of replicates">
+                    <validator type="in_range" message="(1-infinity)" min="1" max="inf"/>
+                </param>
+            </when>
+    </conditional>
+    <param name="constraintfile" type="data" format="text" label="Constraint file" optional="true"/>
+    <conditional name="choose_streefname">
+        <param name="streefname_menu" type="select" label="Source of starting tree and/or model">
+            <option value="stepwise" selected="true">Stepwise</option>
+            <option value="random">Random</option>
+            <option value="file">User Tree</option>
+        </param>
+        <when value="stepwise">
+            <param name="streefname" type="hidden" value="stepwise"/>
+        </when>
+        <when value="random">
+            <param name="streefname" type="hidden" value="random"/>
+        </when>
+        <when value="file">
+            <param name="streefname" format="nexus" type="data" label="Starting Tree File"/>
+        </when>
+    </conditional>
+    <param name="attachmentspertaxon" size="4" type="integer" value="50"
+        label="Attachment branches evaluated per taxon (min=1)" >
+        <validator type="in_range" message="(1-infinity)" min="1" max="inf"/>
+    </param>
+    <param name="randseed" type="text" size="4" value="-1" label="Random Seed (-1 or
+        int)">
+        <validator type="in_range" message="(-1 to infinity)" min="-1" max="inf"/>
+    </param>
+    <param name="availablememory" size="4" value="512" type="integer"
+        label="Available Memory"/>
+    <param name="refinestart" type="select" label="Perform
+        initial rough optimization">
+        <option value="1" selected="true">Yes</option>
+        <option value="0">No</option>
+        </param>
+    <param name="outgroup" type="integer" size="20" value="1" label="Outgroup taxa
+        numbers"/>
+    <param name="collapsebranches" type="select" label="Collapse
+        Branches">
+        <option value="1" selected="true">Yes</option>
+        <option value="0">No</option>
+        </param>
+
+        <conditional name="choose_datatype">
+        <param name="datatype" type="select" label="Model Type">
+            <option value="nucleotide" selected="true">Nucleotide</option>
+            <option value="aminoacid">Amino Acid</option>
+            <option value="codon-aminoacid">Codon-Amino Acid</option>
+            <option value="codon">Codon</option>
+        </param>
+        <when value="nucleotide">
+        <conditional name="choose_ratematrix">
+        <param name="ratematrix" type="select" label="Rate Matrix">
+            <option value="1rate">1rate</option>
+            <option value="2rate">2rate</option>
+            <option value="6rate" selected="true">6rate</option>
+            <option value="fixed">fixed</option>
+            <option value="custom">custom</option>
+        </param>
+            <when value="1rate" />
+            <when value="2rate" />
+            <when value="6rate" />
+            <when value="fixed" />
+            <when value="custom">
+                <param name="ratematrix" type="text" size="20" value="(a b a a b a)" label="Custom Rate Matrix"/>
+            </when>
+        </conditional>
+        <param name="statefrequencies" type="select" label="State
+        Frequencies">
+        <option value="equal">Equal</option>
+        <option value="empirical">Empirical</option>
+        <option value="estimate" selected="true">Estimate</option>
+        <option value="fixed">Fixed</option>
+        </param>
+        <param name="ratehetmodel" type="select" label="Rate Heterogeneity
+        Type">
+        <option value="none">None</option>
+        <option value="gamma" selected="true">Gamma</option>
+        <option value="gammafixed">Gamma Fixed</option>
+        </param>
+    <param name="numratecats" type="integer" size="2" value="4"
+        label="Number of discrete dN/dS categories">
+        <validator type="in_range" message="(1-20)" min="1" max="20"/>
+    </param>
+    <param name="invariantsites" type="select" label="Treatment of
+        proportion of invariable sites parameter">
+        <option value="none">None</option>
+        <option value="estimate" select="true">Estimate</option>
+        <option value="fixed">Fixed</option>
+    </param>
+    </when>
+    <when value="aminoacid">
+        <param name="ratematrix" type="select" label="Rate Matrix">
+            <option value="poisson">Poisson</option>
+            <option value="jones" selected="true">Jones</option>
+            <option value="dayhoff">Dayhoff</option>
+            <option value="wag">WAG</option>
+            <option value="mtmam">mtmam</option>
+            <option value="mtrev">mtREV</option>
+        </param>
+        <param name="statefrequences" type="select" label="Equilibrium Base
+            Frequences">
+            <option value="equal">Equal</option>
+            <option value="empirical" selected="true">Empirical</option>
+            <option value="estimate">Estimate</option>
+            <option value="fixed">Fixed</option>
+            <option value="jones">Jones</option>
+            <option value="dayhoff">Dayhoff</option>
+            <option value="wag">WAG</option>
+            <option value="mtmam">mtmam</option>
+            <option value="mtrev">mtREV</option>
+        </param>
+    <param name="numratecats" type="integer" size="2" value="4"
+        label="Number of discrete dN/dS categories">
+        <validator type="in_range" message="(1-20)" min="1" max="20"/>
+    </param>
+    <param name="invariantsites" type="select" label="Treatment of
+        proportion of invariable sites parameter">
+        <option value="none">None</option>
+        <option value="estimate" select="true">Estimate</option>
+        <option value="fixed">Fixed</option>
+    </param>
+    </when>
+    <when value="codon-aminoacid">
+        <param name="ratematrix" type="select" label="Rate Matrix">
+            <option value="poisson">Poisson</option>
+            <option value="jones" selected="true">Jones</option>
+            <option value="dayhoff">Dayhoff</option>
+            <option value="wag">WAG</option>
+            <option value="mtmam">mtmam</option>
+            <option value="mtrev">mtREV</option>
+        </param>
+        <param name="statefrequences" type="select" label="Equilibrium Base
+            Frequences">
+            <option value="equal">Equal</option>
+            <option value="empirical" selected="true">Empirical</option>
+            <option value="estimate">Estimate</option>
+            <option value="fixed">Fixed</option>
+            <option value="jones">Jones</option>
+            <option value="dayhoff">Dayhoff</option>
+            <option value="wag">WAG</option>
+            <option value="mtmam">mtmam</option>
+            <option value="mtrev">mtREV</option>
+        </param>
+        <param name="geneticcode" type="select" label="Genetic Code">
+            <option value="standard" selected="true">Standard</option>
+            <option value="vertmito">Vertmito</option>
+            <option value="invertmito">Invertmito</option>
+        </param>
+    </when>
+    <when value="codon">
+    <conditional name="choose_ratematrix">
+        <param name="ratematrix" type="select" label="Rate Matrix">
+            <option value="1rate">1rate</option>
+            <option value="2rate">2rate</option>
+            <option value="6rate" selected="true">6rate</option>
+            <option value="fixed">fixed</option>
+            <option value="custom">custom</option>
+        </param>
+            <when value="1rate" />
+            <when value="2rate" />
+            <when value="6rate" />
+            <when value="fixed" />
+            <when value="custom">
+            <param name="ratematrix" type="text" size="20" value="(a b a a b a)" label="Custom Rate Matrix"/>
+        </when>
+    </conditional>
+    <param name="statefrequencies" type="select" label="State
+        Frequencies">
+        <option value="equal">Equal</option>
+        <option value="empirical" selected="true">Empirical</option>
+        <option value="f1x4">F1x4</option>
+        <option value="f3x4">F3x4</option>
+    </param>
+    <param name="ratehetmodel" type="select" label="Rate Heterogeneity
+        Type">
+        <option value="none" selected="true">None</option>
+        <option value="nonsynonymous">Non-synonymous</option>
+    </param>
+    <param name="numratecats" type="integer" size="2" value="1"
+        label="Number of discrete dN/dS categories">
+        <validator type="in_range" message="(1-20)" min="1" max="20"/>
+    </param>
+    <param name="invariantsites" type="hidden" value="none"/>
+    <param name="geneticcode" type="select" label="Genetic Code">
+        <option value="standard" selected="true">Standard</option>
+        <option value="vertmito">Vertmito</option>
+        <option value="invertmito">Invertmito</option>
+    </param>
+    </when>
+    </conditional>
+    <param name="nindivs" type="integer" size="3" value="4" label="Number of individuals in population">
+        <validator type="in_range" message="(2-100)" min="2" max="100"/>
+    </param>
+    <param name="holdover" type="integer" size="2" value="1" label="Unmutated copies of
+        best individual">
+        <validator type="in_range" message="(1-99)" min="1" max="99"/>
+    </param>
+    <param name="selectionintensity" type="float" size="3" value="0.5" label="Strength of
+        selection">
+        <validator type="in_range" message="(0.1-5.0)" min="0.1" max="5.0"/>
+    </param>
+    <param name="holdoverpenalty" type="integer" size="3" value="0" label="Fitness
+        handicap for best individual">
+        <validator type="in_range" message="(0-100)" min="0" max="100"/>
+    </param>
+    <param name="stopgen" type="integer" size="10" value="5000000" label="Maximum number
+        of generations to run">
+        <validator type="in_range" message="(0-50000000)" min="0" max="50000000"/>
+    </param>
+    <param name="stoptime" type="integer" size="10" value="5000000" label="Maximum time to
+        run">
+        <validator type="in_range" message="(0-50000000)" min="0" max="50000000"/>
+    </param>
+    <param name="startoptprec" type="float" size="5" value="0.5" label="Starting
+        optimization precision">
+        <validator type="in_range" message="(0.005-5.0)" min="0.005" max="5.0"/>
+    </param>
+    <param name="minoptprec" type="float" size="5" value="0.01" label="Minimal
+        optimization precision">
+        <validator type="in_range" message="(0.001-5.0)" min="0.001" max="5.0"/>
+    </param>
+    <param name="numberofprecreductions" type="integer" size="3" value="10"
+        label="Number of steps down from Start Precision to Minimum Precision"
+>
+        <validator type="in_range" message="(0-100)" min="0" max="100"/>
+    </param>
+    <param name="treerejectionthreshold" type="float" size="5" value="50.0"
+        label="Tree Rejection Threshold">
+        <validator type="in_range" message="(0-500.0)" min="0" max="500.0"/>
+    </param>
+    <param name="topoweight" type="float" size="10" value="1.0"
+        label="Weight on topology mutations">
+        <validator type="in_range" message="(0-infinity)" min="0" max="inf"/>
+    </param>
+    <param name="modweight" type="float" size="10" value="0.05"
+        label="Weight on model parameter mutations">
+        <validator type="in_range" message="(0-infinity)" min="0" max="inf"/>
+    </param>
+    <param name="brlenweight" type="float" size="10" value="0.2"
+        label="Weight on branch-length parameter mutations">
+        <validator type="in_range" message="(0-infinity)" min="0" max="inf"/>
+    </param>
+    <param name="randnniweight" type="float" size="10" value="0.1"
+        label="Weight on NNI topology changes">
+        <validator type="in_range" message="(0-infinity)" min="0" max="inf"/>
+    </param>
+    <param name="randsprweight" type="float" size="10" value="0.3"
+        label="Weight on SPR topology changes">
+        <validator type="in_range" message="(0-infinity)" min="0" max="inf"/>
+    </param>
+    <param name="limsprweight" type="float" size="10" value="0.6"
+        label="Weight on localized SPR topology changes">
+        <validator type="in_range" message="(0-infinity)" min="0" max="inf"/>
+    </param>
+    <param name="intervallength" type="integer" size="4" value="100"
+        label="Interval Length">
+        <validator type="in_range" message="(0-1000)" min="0" max="1000"/>
+    </param>
+    <param name="intervalstostore" type="integer" size="2" value="5"
+        label="Number of intervals to store">
+        <validator type="in_range" message="(0-1000)" min="0" max="10"/>
+    </param>
+    <param name="limsprrange" type="integer" size="10" value="6"
+        label="Max range for localized SPR topology changes">
+        <validator type="in_range" message="(0-1000)" min="0" max="inf"/>
+    </param>
+    <param name="meanbrlenmuts" type="integer" size="7" value="5"
+        label="Mean number of branch lengths to change per mutation">
+        <validator type="in_range" message="(0-# of taxa)" min="0" max="10000000000"/>
+    </param>
+    <param name="gammashapebrlen" type="integer" size="4" value="1000"
+        label="Magnitude of branch-length mutations">
+        <validator type="in_range" message="(50-2000)" min="50" max="2000"/>
+    </param>
+    <param name="gammashapemodel" type="integer" size="4" value="1000"
+        label="Magnitude of model parameter mutations">
+        <validator type="in_range" message="(50-2000)" min="50" max="2000"/>
+    </param>
+    <param name="uniqueswapbias" type="float" size="4" value="0.1"
+        label="Relative weight assigned to already attempted branch swaps"
+>
+        <validator type="in_range" message="(0.01-1.0)" min="0.01" max="1.0"/>
+    </param>
+    <param name="distanceswapbias" type="float" size="3" value="1.0"
+        label="Relative weight assigned to branch swaps based on locality">
+        <validator type="in_range" message="(0.1-10.0)" min="0.1" max="10.0"/>
+    </param>
+</inputs>
+<outputs>
+    <data format="nexus" name="best_tre" metadata_source="datafname" from_work_dir="garli.best.tre" label="${tool.name} on ${on_string}: garli.best.tre"/>
+    <data format="nexus" name="best_all_tre" metadata_source="datafname" from_work_dir="garli.best.all.tre" label="${tool.name} on ${on_string}: garli.all.best.tre"/>
+    <data format="txt" name="garli_conf" from_work_dir="garli.conf" label="${tool.name} on ${on_string}: garli.conf"/>
+    <data format="txt" name="log00_log" from_work_dir="garli.log00.log" label="${tool.name} on ${on_string}: garli.log00.log"/>
+    <data format="txt" name="screen_log" from_work_dir="garli.screen.log" label="${tool.name} on ${on_string}: garli.screen.log"/>
+</outputs>
+<configfiles>
+<configfile name="garli_conf">
+[general]
+datafname = ${datafname}
+searchreps = ${choose_search_type.searchreps}
+bootstrapreps = ${choose_search_type.bootstrapreps}
+constraintfile = ${constraintfile}
+streefname = ${choose_streefname.streefname}
+attachmentspertaxon = ${attachmentspertaxon}
+ofprefix = garli
+randseed = ${randseed}
+availablememory = ${availablememory}
+logevery = 10
+writecheckpoints = 0
+saveevery = 100
+refinestart = ${refinestart}
+outputeachbettertopology = 0
+outputcurrentbesttopology = 0
+enforcetermconditions = 1
+genthreshfortopoterm = 20000
+scorethreshforterm = 0.05
+significanttopochange = 0.01
+outputphyliptree = 0
+outputmostlyuselessfiles = 0
+restart = 0
+outgroup = ${outgroup}
+resampleproportion = ${choose_search_type.resampleproportion}
+inferinternalstateprobs = 0
+outputsitelikelihoods = 0
+optimizeinputonly = 0
+collapsebranches = ${collapsebranches}
+
+[model1]
+datatype = ${choose_datatype.datatype}
+ratematrix = ${choose_datatype.choose_ratematrix.ratematrix}
+statefrequencies = ${choose_datatype.statefrequencies}
+ratehetmodel = ${choose_datatype.ratehetmodel}
+#if $choose_datatype.numratecats > 0
+numratecats = ${choose_datatype.numratecats}
+#end if
+#if $choose_datatype.invariantsites != ""
+invariantsites = ${choose_datatype.invariantsites}
+#end if
+
+[master]
+nindivs = $nindivs
+holdover = $holdover
+selectionintensity = $selectionintensity
+holdoverpenalty = $holdoverpenalty
+stopgen = $stopgen
+stoptime = $stoptime
+
+startoptprec = $startoptprec
+minoptprec = $minoptprec
+numberofprecreductions = $numberofprecreductions
+treerejectionthreshold = $treerejectionthreshold
+topoweight = $topoweight
+modweight = $modweight
+brlenweight = $brlenweight
+randnniweight = $randnniweight
+randsprweight = $randsprweight
+limsprweight =  $limsprweight
+intervallength = $intervallength
+intervalstostore = $intervalstostore
+limsprrange = $limsprrange
+meanbrlenmuts = $meanbrlenmuts
+gammashapebrlen = $gammashapebrlen
+gammashapemodel = $gammashapemodel
+uniqueswapbias = $uniqueswapbias
+distanceswapbias = 1.0
+</configfile>
+</configfiles>
+
+<help>
+
+**What it does**
+
+GARLI is a program that performs phylogenetic inference using the
+maximum-likelihood criterion. Several sequence types are supported,
+including nucleotide, amino acid and codon. Version 2.0 adds support
+for partitioned models and morphology-like datatypes.
+
+Garli is written and maintained by Derrick Zwickl
+
+Configuration options are adapted from
+https://www.nescent.org/wg_garli/GARLI_Configuration_Settings
+
+-----
+
+**Detailed description of the configuration options**
+
+
+**Analysis Type**
+
+    Specify whether to perform a maximum likelihood search for the best tree, or
+    a bootstrap analysis.
+
+
+**Number of replicates**
+
+    Number of independent search replicates to run.
+
+
+**Relative size of resample data**
+
+    This setting allows for bootstrap-like resampling, but with the
+    psuedoreplicate datasets having the number of alignment columns different
+    from the real data. Setting values below 1.0 is somewhat similar to
+    jackknifing, but not identical.
+
+
+**Attachment branches evaluated per taxon (min=1)**
+
+    The number of attachment branches evaluated for each taxon to be added to
+    the tree during the creation of an ML stepwise-addition starting tree.
+    Briefly, stepwise addition is an algorithm used to make a tree, and involves
+    adding taxa in a random order to a growing tree. For each taxon to be added,
+    a number of randomly chosen attachment branches are tried and scored, and
+    then the best scoring one is chosen as the location of that taxon. This
+    setting controls how many attachment points are evaluated for each taxon to
+    be added. A value of one is equivalent to a completely random tree (only one
+    randomly chosen location is evaluated). A value of greater than 2 times the
+    number of taxa in the dataset means that all attachment points will be
+    evaluated for each taxon, and will result in very good starting trees (but
+    may take a while on large datasets). Even fairly small values (less than 10)
+    can result in starting trees that are much, much better than random, but
+    still fairly different from one another.
+
+
+**Constraint file**
+
+     Select a file containing constraint specifications.
+
+
+**Random seed**
+
+    Random see can have a value of -1 or a positive integer. The random number
+    seed used by the random number generator. Specify “–1” to have a seed chosen
+    for you. Specifying the same seed number in multiple runs will give exactly
+    identical results, if all other parameters and settings are also identical.
+
+
+**Available memory**
+
+    This lets GARLI determine how much system memory it may be able to use to
+    store computations for reuse.
+
+
+**Perform initial rough optimization**
+
+    Specifies whether some initial rough optimization is performed on the
+    starting branch lengths and rate heterogeneity parameters. This is always
+    recommended.
+
+
+**Outgroup taxa numbers**
+
+    The outgroup option allows for orienting tree topologies in a consistent way
+    when they are written to a file. Note that this has NO effect whatsoever on
+    the actual inference and the specified outgroup is NOT constrained to be
+    present in the inferred trees. If multiple outgroup taxa are specified and
+    they do not form a monophyletic group, this setting will be ignored. If you
+    specify a single outgroup taxon it will always be present, and the tree will
+    always be consistently oriented. To specify an outgroup consisting of taxa
+    1, 3 and 5 the format is this: outgroup = 1 3 5. Dashes are used for ranges
+    e.g. 1-3 5.
+
+
+**Collapse branches**
+
+    Before version 1.0, all trees that are returned were fully resolved. This is
+    true even if the maximum-likelihood estimate of some internal branch lengths
+    are effectively zero (or GARLI's minimum, which is 1e-8). In such cases,
+    collapsing the branch into a polytomy would be a better representation. Note
+    that GARLI will never return a tree with an actual branch length of zero,
+    but rather with its minimum value of 1.0e-8. The drawback of always
+    returning fully resolved trees is that what is effectively a polytomy can be
+    resolved in three ways, and different independent searches may randomly
+    return one of those resolutions. Thus, if you compare the trees by topology
+    only, they will look different. If you pay attention to the branch lengths
+    and likelihood scores of the trees it will be apparent that they are
+    effectively the same. I think that collapsing of branches is particularly
+    important when bootstrapping, since no support should be given to a branch
+    that doesn't really exist, i.e., that is a random resolution of a polytomy.
+    Collapsing is also good when calculating tree to tree distances such as the
+    symmetric tree distance, for example when calculating phylogenetic error to
+    a known target tree. Zero-length branches would add to the distances
+    (~error) although they really should not.
+
+
+**Model type**
+
+    The codon-aminoacid datatype means that the data will be supplied as a
+    nucleotide alignment, but will be internally translated and analyzed using
+    an amino acid model. The codon and codon-aminoacid datatypes require
+    nucleotide sequence that is aligned in the correct reading frame. In other
+    words, all gaps in the alignment should be a multiple of 3 in length, and
+    the alignment should start at the first position of a codon. If the
+    alignment has extra columns at the start, middle or end, they should be
+    removed or excluded with a Nexus exset (see the FAQ for an example of exset
+    usage). The correct Genetic Code must also be set.
+
+
+
+
+**Datatype - nucleotide**
+
+**Rate matrix**
+
+    The number of relative substitution rate parameters (note that the number of
+    free parameters is this value minus one). Equivalent to the “nst” setting in
+    PAUP* and MrBayes. 1rate assumes that substitutions between all pairs of
+    nucleotides occur at the same rate (JC model), 2rate allows different rates
+    for transitions and transversions (K2P or HKY models), and 6rate allows a
+    different rate between each nucleotide pair (GTR). These rates are estimated
+    unless the fixed option is chosen. Since version 0.96, parameters for any
+    submodel of the GTR model may be estimated. The format for specifying this
+    is very similar to that used in the “rclass’ setting of PAUP*. Within
+    parentheses, six letters are specified, with spaces between them. The six
+    letters represent the rates of substitution between the six pairs of
+    nucleotides, with the order being A-C, A-G, A-T, C-G, C-T and G-T. Letters
+    within the parentheses that are the same mean that a single parameter is
+    shared by multiple nucleotide pairs.
+
+
+**State frequences**
+
+    Specifies how the equilibrium state frequencies (A, C, G and T) are treated.
+    The empirical setting fixes the frequencies at their observed proportions,
+    and the other options should be self-explanatory.
+
+
+**Datatype - nucleotide or amino-acid**
+
+
+**Treatment of proportion of invariable sites parameter**
+
+    Specifies whether a parameter representing the proportion of sites that are
+    unable to change (i.e. have a substitution rate of zero) will be included.
+    This is typically referred to as 'invariant sites', but would better be
+    termed 'invariable sites'.
+
+
+**Rate heterogeneity type**
+
+    (none, gamma, gammafixed) – The model of rate heterogeneity assumed.
+    “gammafixed” requires that the alpha shape parameter is provided, and a
+    setting of “gamma” estimates it.
+
+
+**Number of discrete dN/dS categories**
+
+    The number of categories of variable rates (not including the invariant site
+    class if it is being used). Must be set to 1 if ratehetmodel is set to none.
+    Note that runtimes and memory usage scale linearly with this setting.
+
+
+**Datatype - amino-acid or codon-aminoacid**
+
+**Rate matrix**
+
+    (poisson, jones, dayhoff, wag, mtmam, mtrev) – The fixed amino acid rate
+    matrix to use. You should use the matrix that gives the best likelihood, and
+    could use a program like PROTTEST (very much like MODELTEST, but for amino
+    acid models) to determine which fits best for your data. Poisson assumes a
+    single rate of substitution between all amino acid pairs, and is a very poor
+    model.
+
+
+**Equilibrium Base Frequences **
+
+    (equal, empirical, estimate, fixed, jones, dayhoff, wag, mtmam, mtrev) –
+    Specifies how the equilibrium state frequencies of the 20 amino acids are
+    treated. The “empirical” option fixes the frequencies at their observed
+    proportions (when describing a model this is often termed '+F').
+
+
+**Number of discrete dN/dS categories**
+
+    The number of categories of variable rates (not including the invariant site
+    class if it is being used). Must be set to 1 if ratehetmodel is set to none.
+    Note that runtimes and memory usage scale linearly with this setting.
+
+
+**Treatment of proportion of invariable sites parameter**
+
+    Specifies whether a parameter representing the proportion of sites that are
+    unable to change (i.e. have a substitution rate of zero) will be included.
+    This is typically referred to as 'invariant sites', but would better be
+    termed 'invariable sites'.
+
+
+**Datatype - codon**
+
+
+**Rate matrix**
+
+    (1rate, 2rate, 6rate, fixed, custom string) – This determines the relative
+    rates of nucleotide substitution assumed by the codon model. The options are
+    exactly the same as those allowed under a normal nucleotide model. A codon
+    model with ratematrix = 2rate specifies the standard Goldman and Yang (1994)
+    model, with different substitution rates for transitions and transversions.
+
+
+**State frequences**
+
+    The options are to use equal codon frequencies (not a good option), the
+    frequencies observed in your dataset (termed “empirical” in GARLI), or the
+    codon frequencies implied by the “F1x4” or “F3x4” methods (using PAML
+    terminology). These last two options calculate the codon frequencies as the
+    product of the frequencies of the three nucleotides that make up each codon.
+    In the “F1x4” case the nucleotide frequencies are those observed in the
+    dataset across all codon positions, while the “F3x4” option uses the
+    nucleotide frequencies observed in the data at each codon position
+    separately.
+
+
+**Rate Heterogeneity Type**
+
+    For codon models, the default is to infer a single dN/dS parameter.
+    Alternatively, a model can be specified that infers a given number of dN/dS
+    categories, with the dN/dS values and proportions falling in each category
+    estimated (ratehetmodel = nonsynonymous). This is the 'discrete' or 'M3'
+    model of Yang et al., 2000.
+
+
+**Number of discrete dN/dS categories**
+
+    When ratehetmodel = nonsynonymous, this is the number of dN/dS parameter
+    categories.
+
+
+**Datatype - codon or codon-aminoacid**
+
+
+**Genetic code**
+
+    The genetic code to be used in translating codons into amino acids.
+
+
+**Population Settings**
+
+
+**Number of individuals in population**
+
+    The number of individuals in the population. This may be increased, but
+    doing so is generally not beneficial. Note that typical genetic algorithms
+    tend to have much, much larger population sizes than GARLI defaults.
+
+
+**Unmutated copies of best individual**
+
+    The number of times the best individual is copied to the next generation
+    with no chance of mutation. It is best not to mess with this setting.
+
+
+**Strength of selection**
+
+    Controls the strength of selection, with larger numbers denoting stronger
+    selection. The relative probability of reproduction of two individuals
+    depends on the difference in their log likelihoods (ΔlnL) and is formulated
+    very similarly to the procedure of calculating Akaike weights.
+
+
+**Fitness handicap for the best individual**
+
+    This can be used to bias the probability of reproduction of the best
+    individual downward. Because the best individual is automatically copied
+    into the next generation, it has a bit of an unfair advantage and can cause
+    all population variation to be lost due to genetic drift, especially with
+    small populations sizes. The value specified here is subtracted from the
+    best individual’s lnL score before calculating the probabilities of
+    reproduction. It seems plausible that this might help maintain variation,
+    but I have not seen it cause a measurable effect.
+
+
+**Maximum number of generations to run**
+
+    Use if automatic termination is desired to prevent a runaway process.
+
+
+**Maximum time to run**
+
+    The maximum number of seconds for the run to continue. Use if automatic
+    termination is desired to prevent a runaway process.
+
+
+**Branch-length optimization settings**
+
+
+**Minimal optimization precision**
+
+    The minimum allowed value of the optimization precision - must not be larger
+    then the Starting optimization precision.
+
+
+**Number of steps down from Start Precision to Minimum Precision**
+
+    Specify the number of steps that it will take for the optimization precision
+    to decrease (linearly) from startoptrec to minoptprec.
+
+
+**Tree rejection threshold**
+
+    This setting controls which trees have more extensive branch-length
+    optimization applied to them. All trees created by a branch swap receive
+    optimization on a few branches that directly took part in the rearrangement.
+    If the difference in score between the partially optimized tree and the best
+    known tree is greater than treerejectionthreshold, no further optimization
+    is applied to the branches of that tree. Reducing this value can
+    significantly reduce runtimes, often with little or no effect on results.
+    However, it is possible that a better tree could be missed if this is set
+    too low. In cases in which obtaining the very best tree per search is not
+    critical (e.g., bootstrapping), setting this lower (~20) is probably safe.
+
+
+**Settings controlling the proportions of the mutation types**
+
+
+**Weight on topology mutations**
+
+    The prior weight assigned to the class of topology mutations (NNI, SPR and
+    limSPR). Note that setting this to 0.0 turns off topology mutations, meaning
+    that the tree topology is fixed for the run. This used to be a way to have
+    the program estimate only model parameters and branch-lengths, but the
+    optimizeinputonly setting is now a better way to go.
+
+
+**Weight on model parameter mutations**
+
+    The prior weight assigned to the class of model mutations. Note that setting
+    this at 0.0 fixes the model during the run.
+
+
+**Weight on branch-length parameter mutations**
+
+    The prior weight assigned to branch-length mutations. The same procedure
+    used above to determine the proportion of Topology:Model:Branch-Length
+    mutations is also used to determine the relative proportions of the three
+    types of topological mutations (NNI:SPR:limSPR), controlled by the following
+    three weights. Note that the proportion of mutations applied to each of the
+    model parameters is not user controlled.
+
+
+**Weight on NNI topology changes**
+
+    The prior weight assigned to NNI mutations
+
+
+**Weight on SPR topology changes**
+
+    The prior weight assigned to random SPR mutations. For very large datasets
+    it is often best to set this to 0.0, as random SPR mutations essentially
+    never result in score increases.
+
+
+**Weight on localized SPR topology changes**
+
+    The prior weight assigned to SPR mutations with the reconnection branch
+    limited to being a maximum of limsprrange branches away from where the
+    branch was detached.
+
+
+**Interval Length**
+
+    The number of generations in each interval during which the number and
+    benefit of each mutation type are stored.
+
+
+**Number of intervals to store**
+
+    The number of intervals to be stored. Thus, records of mutations are kept
+    for the last (intervallength x intervalstostore) generations. Every
+    intervallength generations the probabilities of the mutation types are
+    updated by the scheme described above.
+
+
+**Settings controlling mutation details**
+
+
+**Max range for localized SPR topology changes**
+
+    The maximum number of branches away from its original location that a branch
+    may be reattached during a limited SPR move. Setting this too high (&gt; 10)
+    can seriously degrade performance, but if you do so in conjunction with a
+    large increase in genthreshfort.
+
+
+**Settings controlling mutation details**
+
+    The mean of the binomial distribution from which the number of branch
+    lengths mutated is drawn during a branch length mutation.
+
+
+**Magnitude of branch-length mutations**
+
+    The shape parameter of the gamma distribution (with a mean of 1.0) from
+    which the branch-length multipliers are drawn for branch-length mutations.
+    Larger numbers cause smaller changes in branch lengths. (Note that this has
+    nothing to do with gamma rate heterogeneity.)
+
+
+**Magnitude of model parameter mutations**
+
+    The shape parameter of the gamma distribution (with a mean of 1.0) from
+    which the model mutation multipliers are drawn for model parameters
+    mutations. Larger numbers cause smaller changes in model parameters. (Note
+    that this has nothing to do with gamma rate heterogeneity.)
+
+
+**Relative weight assigned to already attempted branch swaps**
+
+    With version 0.95 and later, GARLI keeps track of which branch swaps it has
+    attempted on the current best tree. Because swaps are applied randomly, it
+    is possible that some swaps are tried twice before others are tried at all.
+    This option allows the program to bias the swaps applied toward those that
+    have not yet been attempted. Each swap is assigned a relative weight
+    depending on the number of times that it has been attempted on the current
+    best tree. This weight is equal to (uniqueswapbias) raised to the (# times
+    swap attempted) power. In other words, a value of 0.5 means that swaps that
+    have already been tried once will be half as likely as those not yet
+    attempted, swaps attempted twice will be ¼ as likely, etc. A value of 1.0
+    means no biasing. Use of this option may allow the use of somewhat larger
+    values of limsprrange.
+
+
+**Relative weight assigned to branch swaps based on locality**
+
+    This option is similar to uniqueswapbias, except that it biases toward
+    certain swaps based on the topological distance between the initial and
+    rearranged trees. The distance is measured as in the limsprrange, and is
+    half the the Robinson-Foulds distance between the trees. As with
+    uniqueswapbias, distanceswapbias assigns a relative weight to each potential
+    swap. In this case the weight is (distanceswapbias) raised to the
+    (reconnection distance - 1) power. Thus, given a value of 0.5, the weight of
+    an NNI is 1.0, the weight of an SPR with distance 2 is 0.5, with distance 3
+    is 0.25, etc. Note that values less than 1.0 bias toward more localized
+    swaps, while values greater than 1.0 bias toward more extreme swaps. Also
+    note that this bias is only applied to limSPR rearrangements. Be careful in
+    setting this, as extreme values can have a very large effect.
+
+</help>
+</tool>