BEAST 2.x Starting Tree
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Nathan Lujan
May 27, 2015, 12:21:53 PM5/27/15
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I've noticed that the <init> block in BEAST 2.2 and 2.3 .xml files differs in some confusing ways from the <init> blocks quoted in most online tutorials for how to insert a starting tree. Copied below is the <init> block from a recent v2.3 .xml file:
<init id="RandomTree.t:tree" spec="beast.evolution.tree.RandomTree" estimate="false" initial="@Tree.t:tree">
<taxa id="myh63rdpos" spec="FilteredAlignment" data="@257taxa_concat_w_BayesBlock" filter="3633-4293\3"/>
<populationModel id="ConstantPopulation0.t:tree" spec="ConstantPopulation"> <parameter id="randomPopSize.t:tree" name="popSize">1.0</parameter> </populationModel>
I am confused by insertion in this block of my last data partition (i.e., myh63rdpos; 3633-4293\3).
At any rate, to insert a starting tree, I have tried commenting out that entire <init> section and pasting in the following:
<init spec="beast.util.TreeParser" id='NewickTree.t:UNIQUE_FILENAME' initial="@Tree.t:tree" taxa='@ALIGNMENT_NAME' IsLabelledNewick="true" newick="NEWICK TREE HERE"/>
This unfortunately introduces an error related to "treeLikelihood.myh63rdpos". Any suggestions for how to resolve this would be appreciated.
Thanks, Nathan
Remco Bouckaert
May 27, 2015, 3:43:03 PM5/27/15
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Hi Nathan,
By replacing the block, you accidentally removed the alignment for your last partition, so the treelikelihood cannot find it.
If you copy
<taxa id="myh63rdpos" spec="FilteredAlignment" data="@257taxa_concat_w_BayesBlock" filter="3633-4293\3"/>
just before the run-tag (<run id=“mcmc"..>) the treelikelihood should be able to find the alignment it is looking for.
Hope this helps,
Remco
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Nathan Lujan
May 27, 2015, 5:58:04 PM5/27/15
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Thanks Remco, yes, that got myself and a colleague over our starting tree hurdle!
Unfortunately, we are now both encountering the following error message:
java.lang.Exception: Could not find a proper state to initialise. Perhaps try another seed.
at beast.core.MCMC.run(Unknown Source)
at beast.app.BeastMCMC.run(Unknown Source)
at beast.app.beastapp.BeastMain.<init>(Unknown Source)
at beast.app.beastapp.BeastMain.main(Unknown Source)
at beast.app.beastapp.BeastLauncher.main(Unknown Source)
Do you have any suggestions for how to overcome this?
Thanks, Nathan
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Nathan K. Lujan, PhD
Assistant Editor, Journal of Fish Biology
Phone: 615-579-7234 | Email: nkl...@gmail.com |
Webpage: http://loricariidae.org
Remco Bouckaert
May 27, 2015, 6:03:37 PM5/27/15
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Hi Nathan,
It should print out some information about which part of the posterior is not valid (should have -Infinity next to it).
Without the rest of the output it is hard to tell, but the most common cause is that the starting tree is not compatible with calibrations, in which case one of the calibrations has -Infinity next to it in the output.
Cheers,
Remco
Nathan Lujan
May 27, 2015, 6:16:23 PM5/27/15
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I’ve attached the complete output at bottom. Infinity appears at two different points in the output, excerpted here:
First:
Start likelihood: -Infinity after 10 initialisation attempts
P(posterior) = -Infinity (was NaN)
P(prior) = -Infinity (was NaN)
Second:
P(Ancistrus.prior) = -Infinity (was NaN)
The Ancistrus prior is set as a log normal distribution with an offset of 12.8 and mean and sigma left at default (1, 1.25).
Complete output:
File: Loricalibration4_starttree.xml seed: 1432764677121 threads: 1
WARNING: Yule Model cannot handle dated tips. Use for example a coalescent prior instead.
Ignoring ambiguities in tree likelihood.
With 258 unique site patterns.
Using rescaling scheme : dynamic
Ignoring ambiguities in tree likelihood.
With 209 unique site patterns.
Using rescaling scheme : dynamic
Ignoring ambiguities in tree likelihood.
With 131 unique site patterns.
Using rescaling scheme : dynamic
Using BEAGLE version: 1.x resource 0: CPU
with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU
Using BEAGLE version: 1.x resource 0: CPU
with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU
Using BEAGLE version: 1.x resource 0: CPU
with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU
Ignoring ambiguities in tree likelihood.
With 380 unique site patterns.
Using rescaling scheme : dynamic
Ignoring ambiguities in tree likelihood.
With 174 unique site patterns.
Using rescaling scheme : dynamic
Ignoring ambiguities in tree likelihood.
With 114 unique site patterns.
Using rescaling scheme : dynamic
Ignoring ambiguities in tree likelihood.
With 314 unique site patterns.
Using rescaling scheme : dynamic
Ignoring ambiguities in tree likelihood.
With 196 unique site patterns.
Using rescaling scheme : dynamic
Using BEAGLE version: 1.x resource 0: CPU
with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU
Using BEAGLE version: 1.x resource 0: CPU
with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU
Using BEAGLE version: 1.x resource 0: CPU
with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU
Using BEAGLE version: 1.x resource 0: CPU
with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU
Using BEAGLE version: 1.x resource 0: CPU
with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU
Using BEAGLE version: 1.x resource 0: CPU
with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH Ignoring ambiguities in tree likelihood.
With 132 unique site patterns.
Using rescaling scheme : dynamic
Ignoring ambiguities in tree likelihood.
With 294 unique site patterns.
Using rescaling scheme : dynamic
Ignoring ambiguities in tree likelihood.
With 30 unique site patterns.
Using rescaling scheme : dynamic
Ignoring ambiguities in tree likelihood.
With 201 unique site patterns.
Using rescaling scheme : dynamic
Ignoring ambiguities in tree likelihood.
With 51 unique site patterns.
Using rescaling scheme : dynamic
Start likelihood: -Infinity after 10 initialisation attempts
P(posterior) = -Infinity (was NaN)
P(prior) = -Infinity (was NaN)
P(YuleModel.t:tree) = -374.3126965269218 (was NaN)
P(YuleBirthRatePrior.t:tree) = 0.0 (was NaN)
P(PropInvariantPrior.s:cytb1stpos) = 0.0 (was NaN)
P(PropInvariantPrior.s:cytb2ndpos) = 0.0 (was NaN)
P(PropInvariantPrior.s:cytb3rdpos) = 0.0 (was NaN)
P(PropInvariantPrior.s:myh61stpos) = 0.0 (was NaN)
P(PropInvariantPrior.s:myh63r EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU
Using BEAGLE version: 1.x resource 0: CPU
with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU
Using BEAGLE version: 1.x resource 0: CPU
with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU
Using BEAGLE version: 1.x resource 0: CPU
with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU
Using BEAGLE version: 1.x resource 0: CPU
with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU
dpos) = 0.0 (was NaN)
P(PropInvariantPrior.s:noncoding) = 0.0 (was NaN)
P(PropInvariantPrior.s:rag11stpos) = 0.0 (was NaN)
P(PropInvariantPrior.s:rag12ndpos) = 0.0 (was NaN)
P(PropInvariantPrior.s:rag21stpos) = 0.0 (was NaN)
P(PropInvariantPrior.s:rag22ndpos) = 0.0 (was NaN)
P(RateACPrior.s:cytb1stpos) = -3.184008455701433 (was NaN)
P(RateACPrior.s:cytb2ndpos) = -3.184008455701433 (was NaN)
P(RateACPrior.s:cytb3rdpos) = -3.184008455701433 (was NaN)
P(RateACPrior.s:myh61stpos) = -3.184008455701433 (was NaN)
P(RateACPrior.s:myh62ndpos) = -3.184008455701433 (was NaN)
P(RateACPrior.s:myh63rdpos) = -3.184008455701433 (was NaN)
P(RateACPrior.s:noncoding) = -3.184008455701433 (was NaN)
P(RateACPrior.s:rag11stpos) = -3.184008455701433 (was NaN)
P(RateACPrior.s:rag12ndpos) = -3.184008455701433 (was NaN)
P(RateACPrior.s:rag13rdpos) = -3.184008455701433 (was NaN)
P(RateACPrior.s:rag21stpos) = -3.184008455701433 (was NaN)
P(RateACPrior.s:rag22ndpos) = -3.184008455701433 (was NaN)
P(RateACPrior.s:rag23rdpos) = -3.184008455701433 (was NaN)
P(RateAGPrior.s:cytb1stpos) = -3.1686658147294304 (was NaN)
P(RateAGPrior.s:cytb2ndpos) = -3.184008455701433 (was NaN)
P(RateAGPrior.s:cytb3rdpos) = -3.184008455701433 (was NaN)
P(RateAGPrior.s:myh61stpos) = -3.184008455701433 (was NaN)
P(RateAGPrior.s:myh62ndpos) = -3.184008455701433 (was NaN)
P(RateAGPrior.s:myh63rdpos) = -3.184008455701433 (was NaN)
P(RateAGPrior.s:noncoding) = -3.184008455701433 (was NaN)
P(RateAGPrior.s:rag11stpos) = -3.184008455701433 (was NaN)
P(RateAGPrior.s:rag12ndpos) = -3.184008455701433 (was NaN)
P(RateAGPrior.s:rag13rdpos) = -3.184008455701433 (was NaN)
P(RateAGPrior.s:rag21stpos) = -3.184008455701433 (was NaN)
P(RateAGPrior.s:rag22ndpos) = -3.184008455701433 (was NaN)
P(RateAGPrior.s:rag23rdpos) = -3.184008455701433 (was NaN)
P(RateATPrior.s:cytb1stpos) = -3.184008455701433 (was NaN)
P(RateATPrior.s:cytb2ndpos) = -3.184008455701433 (was NaN)
P(RateATPrior.s:cytb3rdpos) = -3.184008455701433 (was NaN)
P(RateATPrior.s:myh61stpos) = -3.184008455701433 (was NaN)
P(RateATPrior.s:myh62ndpos) = -3.184008455701433 (was NaN)
P(RateATPrior.s:myh63rdpos) = -3.184008455701433 (was NaN)
P(RateATPrior.s:noncoding) = -3.184008455701433 (was NaN)
P(RateATPrior.s:rag11stpos) = -3.184008455701433 (was NaN)
P(RateATPrior.s:rag12ndpos) = -3.184008455701433 (was NaN)
P(RateATPrior.s:rag13rdpos) = -3.184008455701433 (was NaN)
P(RateATPrior.s:rag21stpos) = -3.184008455701433 (was NaN)
P(RateATPrior.s:rag22ndpos) = -3.184008455701433 (was NaN)
P(RateATPrior.s:rag23rdpos) = -3.184008455701433 (was NaN)
P(RateCGPrior.s:cytb1stpos) = -3.184008455701433 (was NaN)
P(RateCGPrior.s:cytb2ndpos) = -3.184008455701433 (was NaN)
P(RateCGPrior.s:cytb3rdpos) = -3.184008455701433 (was NaN)
P(RateCGPrior.s:myh61stpos) = -3.184008455701433 (was NaN)
P(RateCGPrior.s:myh62ndpos) = -3.184008455701433 (was NaN)
P(RateCGPrior.s:myh63rdpos) = -3.184008455701433 (was NaN)
P(RateCGPrior.s:noncoding) = -3.184008455701433 (was NaN)
P(RateCGPrior.s:rag11stpos) = -3.184008455701433 (was NaN)
P(RateCGPrior.s:rag12ndpos) = -3.184008455701433 (was NaN)
P(RateCGPrior.s:rag13rdpos) = -3.184008455701433 (was NaN)
P(RateCGPrior.s:rag21stpos) = -3.184008455701433 (was NaN)
P(RateCGPrior.s:rag22ndpos) = -3.184008455701433 (was NaN)
P(RateCGPrior.s:rag23rdpos) = -3.184008455701433 (was NaN)
P(RateGTPrior.s:cytb1stpos) = -3.184008455701433 (was NaN)
P(RateGTPrior.s:cytb2ndpos) = -3.184008455701433 (was NaN)
P(RateGTPrior.s:cytb3rdpos) = -3.184008455701433 (was NaN)
P(RateGTPrior.s:myh61stpos) = -3.184008455701433 (was NaN)
P(RateGTPrior.s:myh62ndpos) = -3.184008455701433 (was NaN)
P(RateGTPrior.s:myh63rdpos) = -3.184008455701433 (was NaN)
P(RateGTPrior.s:noncoding) = -3.184008455701433 (was NaN)
P(RateGTPrior.s:rag11stpos) = -3.184008455701433 (was NaN)
P(RateGTPrior.s:rag12ndpos) = -3.184008455701433 (was NaN)
P(RateGTPrior.s:rag13rdpos) = -3.184008455701433 (was NaN)
P(RateGTPrior.s:rag21stpos) = -3.184008455701433 (was NaN)
P(RateGTPrior.s:rag22ndpos) = -3.184008455701433 (was NaN)
P(RateGTPrior.s:rag23rdpos) = -3.184008455701433 (was NaN)
P(MeanRatePrior.c:clock) = 0.0 (was NaN)
P(ucldStdevPrior.c:clock) = 0.819364145120802 (was NaN)
P(Ancistrus.prior) = -Infinity (was NaN)
P(Callichthyidae.prior) = NaN (was NaN)
P(Isorineloricara-Spectracanthicus.prior) = NaN (was NaN)
P(Loricarioidea.prior) = NaN (was NaN)
P(Panaque.prior) = NaN (was NaN)
P(transAndean_Cordylancistrus.prior) = NaN (was NaN)
P(likelihood) = NaN (was NaN)
P(treeLikelihood.noncoding) = NaN (was NaN)
P(treeLikelihood.cytb1stpos) = NaN (was NaN)
P(treeLikelihood.cytb2ndpos) = NaN (was NaN)
P(treeLikelihood.cytb3rdpos) = NaN (was NaN)
P(treeLikelihood.rag11stpos) = NaN (was NaN)
P(treeLikelihood.rag12ndpos) = NaN (was NaN)
P(treeLikelihood.rag13rdpos) = NaN (was NaN)
P(treeLikelihood.rag21stpos) = NaN (was NaN)
P(treeLikelihood.rag22ndpos) = NaN (was NaN)
P(treeLikelihood.rag23rdpos) = NaN (was NaN)
P(treeLikelihood.myh61stpos) = NaN (was NaN)
P(treeLikelihood.myh62ndpos) = NaN (was NaN)
P(treeLikelihood.myh63rdpos) = NaN (was NaN)
java.lang.Exception: Could not find a proper state to initialise. Perhaps try another seed.
at beast.core.MCMC.run(Unknown Source)
at beast.app.BeastMCMC.run(Unknown Source)
at beast.app.beastapp.BeastMain.<init>(Unknown Source)
at beast.app.beastapp.BeastMain.main(Unknown Source)
at beast.app.beastapp.BeastLauncher.main(Unknown Source)
Remco Bouckaert
May 27, 2015, 6:19:15 PM5/27/15
to beast...@googlegroups.com
This is causing the problem:
On 28/05/2015, at 10:16 am, Nathan Lujan <nkl...@gmail.com> wrote:
P(Ancistrus.prior) = -Infinity (was NaN)
You want to check the starting tree is compatible with this calibration — check that the taxonset is monophyletic if you specified that, and also check whether the height of the clade in the starting tree is compatible with the range of the calibration.
Cheers,
Remco
hanlie
Dec 20, 2016, 9:17:18 AM12/20/16
to beast-users
Hi Remco
I 'managed' to get passed the starting-tree issues, but are now stuck with the following error;
" Error 123 parsing the xml input file Input 101: type mismatch for input log. beast.core.Loggable.isAssignableFrom(class beast.evolution.alignment.TaxonSet)=false expected 'Loggable' but got 'TaxonSet' "
I changed the weights of the subtreeslide, wide, narrow and Winsonbalding operators to zero to maintain a fixed topology.... but have no idea what the aforementioned error is telling me. Can you please advise? I am pasting the xml section that follows the sequence data below;
<map name="Uniform" >beast.math.distributions.Uniform</map>
<map name="Exponential" >beast.math.distributions.Exponential</map>
<map name="LogNormal" >beast.math.distributions.LogNormalDistributionModel</map>
<map name="Normal" >beast.math.distributions.Normal</map>
<map name="Beta" >beast.math.distributions.Beta</map>
<map name="Gamma" >beast.math.distributions.Gamma</map>
<map name="LaplaceDistribution" >beast.math.distributions.LaplaceDistribution</map>
<map name="prior" >beast.math.distributions.Prior</map>
<map name="InverseGamma" >beast.math.distributions.InverseGamma</map>
<map name="OneOnX" >beast.math.distributions.OneOnX</map>
<run id="mcmc" spec="MCMC" chainLength="100000000">
<state id="state" storeEvery="5000">
<tree id="Tree.t:ck-hme-reducedCYTB" name="stateNode">
<taxonset id="TaxonSet.ck-hme-reducedCYTB" spec="TaxonSet">
<alignment idref="ck-hme-reducedCYTB"/>
</taxonset>
</tree>
<stateNode id="RBcount.s:ck-hme-reducedCYTB" spec="parameter.IntegerParameter" lower="0" upper="5">5</stateNode>
<parameter id="RBrates.s:ck-hme-reducedCYTB" dimension="5" lower="0.01" name="stateNode" upper="100.0">1.0</parameter>
<stateNode id="RBcount.s:ck-hme-reducedCMOS4" spec="parameter.IntegerParameter" lower="0" upper="5">5</stateNode>
<parameter id="RBrates.s:ck-hme-reducedCMOS4" dimension="5" lower="0.01" name="stateNode" upper="100.0">1.0</parameter>
<stateNode id="RBcount.s:ck-hme-reducedND4" spec="parameter.IntegerParameter" lower="0" upper="5">5</stateNode>
<parameter id="RBrates.s:ck-hme-reducedND4" dimension="5" lower="0.01" name="stateNode" upper="100.0">1.0</parameter>
<parameter id="mutationRate.s:ck-hme-reducedCYTB" name="stateNode">1.0</parameter>
<parameter id="gammaShape.s:ck-hme-reducedCYTB" name="stateNode">1.0</parameter>
<parameter id="mutationRate.s:ck-hme-reducedCMOS4" name="stateNode">0.1</parameter>
<parameter id="gammaShape.s:ck-hme-reducedCMOS4" name="stateNode">1.0</parameter>
<parameter id="mutationRate.s:ck-hme-reducedND4" name="stateNode">1.0</parameter>
<parameter id="gammaShape.s:ck-hme-reducedND4" name="stateNode">1.0</parameter>
<parameter id="ucldStdev.c:ck-hme-reducedCYTB" lower="0.0" name="stateNode">0.1</parameter>
<stateNode id="rateCategories.c:ck-hme-reducedCYTB" spec="parameter.IntegerParameter" dimension="196">1</stateNode>
<parameter id="ucldStdev.c:ck-hme-reducedCMOS4" lower="0.0" name="stateNode">0.1</parameter>
<stateNode id="rateCategories.c:ck-hme-reducedCMOS4" spec="parameter.IntegerParameter" dimension="196">1</stateNode>
<parameter id="ucldStdev.c:ck-hme-reducedND4" lower="0.0" name="stateNode">0.1</parameter>
<stateNode id="rateCategories.c:ck-hme-reducedND4" spec="parameter.IntegerParameter" dimension="196">1</stateNode>
<parameter id="birthRate.t:ck-hme-reducedCYTB" name="stateNode">1.0</parameter>
</state>
<init spec="beast.util.TreeParser" id="StartingTree.t:ck-hme-reducedCYTB" initial="@Tree.t:ck-hme-reducedCYTB" taxa="@ck-hme-reducedCYTB" IsLabelledNewick="true" adjustTipHeights="false"
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<taxon idref="Shinisaurus_crocodilarius"/>
</taxonset>
<LogNormal id="LogNormalDistributionModel.0111" name="distr" offset="4.65">
<parameter id="RealParameter.021" estimate="false" name="M">4.44</parameter>
<parameter id="RealParameter.022" estimate="false" lower="0.0" name="S" upper="5.0">0.08</parameter>
</LogNormal>
</distribution>
<distribution id="c4.prior" spec="beast.math.distributions.MRCAPrior" monophyletic="true" tree="@Tree.t:ck-hme-reducedCYTB">
<taxonset id="c4" spec="TaxonSet">
<taxon idref="631120"/>
<taxon idref="631245"/>
<taxon idref="759"/>
<taxon idref="Acrochordus_granulatus"/>
<taxon idref="Afronatrix_anscopus"/>
<taxon idref="Agkistrodon_piscivorus"/>
<taxon idref="Alsophis_portoricensis"/>
<taxon idref="Amblyodipsas_dimidiata"/>
<taxon idref="Amplorhinus_multimaculatus_PEM"/>
<taxon idref="Aspidelaps_scutatus"/>
<taxon idref="Atheris_nitschei"/>
<taxon idref="B_forst"/>
<taxon idref="Boa_constrictor"/>
<taxon idref="Boiga_dendrophila"/>
<taxon idref="Buhoma_procterae"/>
<taxon idref="Bungarus_fasciatus"/>
<taxon idref="Calliophis_bivirgatus"/>
<taxon idref="Cemophora_coccinea"/>
<taxon idref="Coluber_dorri"/>
<taxon idref="Coronella_girondica"/>
<taxon idref="Crotalus_viridis"/>
<taxon idref="D_unicolo"/>
<taxon idref="Demansia_atra"/>
<taxon idref="Dendroaspis_polylepis"/>
<taxon idref="Dipsina_multimaculata"/>
<taxon idref="Dispholidus_typus"/>
<taxon idref="Ditypophis_vivax"/>
<taxon idref="Duberria_lutrix"/>
<taxon idref="EBG1363"/>
<taxon idref="EBG2607"/>
<taxon idref="EBG2610"/>
<taxon idref="EBG2673"/>
<taxon idref="EI_138"/>
<taxon idref="EI_166"/>
<taxon idref="EI_72"/>
<taxon idref="ELI373"/>
<taxon idref="ELI509"/>
<taxon idref="ELI510"/>
<taxon idref="ELIPEMR18"/>
<taxon idref="E_auro"/>
<taxon idref="FFNR002"/>
<taxon idref="Grayia_tholloni"/>
<taxon idref="HB282"/>
<taxon idref="Hemorrhois_hippocrepis"/>
<taxon idref="Hemorrhois_ravergieri"/>
<taxon idref="Hypsiglena_torquata"/>
<taxon idref="JM01442"/>
<taxon idref="Lycodon"/>
<taxon idref="Lycophidion_capense"/>
<taxon idref="MBUR03179"/>
<taxon idref="MBUR03481"/>
<taxon idref="MBUR08097"/>
<taxon idref="MBUR08206"/>
<taxon idref="MBUR8574"/>
<taxon idref="MOZ14_298"/>
<taxon idref="MTSN10482"/>
<taxon idref="MTSN7300"/>
<taxon idref="MTSN7373"/>
<taxon idref="MTSN8200"/>
<taxon idref="Madagascarophis_colubrinus"/>
<taxon idref="Micrelaps_bicoloratus"/>
<taxon idref="Naja_kaouthia"/>
<taxon idref="Naja_multifasciata"/>
<taxon idref="Naja_nivea"/>
<taxon idref="Natrix_natrix"/>
<taxon idref="Ophiophagus_hannah"/>
<taxon idref="Oxyrhabdium_leporinum"/>
<taxon idref="Platyceps_florulentus"/>
<taxon idref="Psammodynastes_pulverulentus"/>
<taxon idref="Psammophis"/>
<taxon idref="Pseudaspis_cana"/>
<taxon idref="Ptyas_mucosus"/>
<taxon idref="Ramphotyphlops_braminus"/>
<taxon idref="Rhamphiophis_rostratus"/>
<taxon idref="SPN091"/>
<taxon idref="TGET1-67"/>
<taxon idref="T_sem"/>
<taxon idref="Thamnophis_sirtalis"/>
<taxon idref="Thom605"/>
<taxon idref="Thom637"/>
<taxon idref="Tyr01"/>
<taxon idref="WC-ANG001"/>
<taxon idref="WC12-A082"/>
<taxon idref="WC12-A109"/>
<taxon idref="WC12_A136"/>
<taxon idref="WC3903"/>
<taxon idref="WCDNA0087"/>
<taxon idref="WCDNA816"/>
<taxon idref="WRB933"/>
<taxon idref="Walterinnesia_aegyptia"/>
<taxon idref="jes567"/>
<taxon idref="jes592"/>
<taxon idref="jes621"/>
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<LogNormal id="LogNormalDistributionModel.02" name="distr" offset="4.79">
<parameter id="RealParameter.023" estimate="false" name="M">4.6</parameter>
<parameter id="RealParameter.024" estimate="false" lower="0.0" name="S" upper="5.0">0.07</parameter>
</LogNormal>
</distribution>
<distribution id="c5.prior" spec="beast.math.distributions.MRCAPrior" monophyletic="true" tree="@Tree.t:ck-hme-reducedCYTB">
<taxonset id="c5" spec="TaxonSet">
<taxon idref="631120"/>
<taxon idref="631245"/>
<taxon idref="759"/>
<taxon idref="Acrochordus_granulatus"/>
<taxon idref="Afronatrix_anscopus"/>
<taxon idref="Agkistrodon_piscivorus"/>
<taxon idref="Alsophis_portoricensis"/>
<taxon idref="Amblyodipsas_dimidiata"/>
<taxon idref="Amplorhinus_multimaculatus_PEM"/>
<taxon idref="Aspidelaps_scutatus"/>
<taxon idref="Atheris_nitschei"/>
<taxon idref="B_forst"/>
<taxon idref="Boiga_dendrophila"/>
<taxon idref="Buhoma_procterae"/>
<taxon idref="Bungarus_fasciatus"/>
<taxon idref="Calliophis_bivirgatus"/>
<taxon idref="Cemophora_coccinea"/>
<taxon idref="Coluber_dorri"/>
<taxon idref="Coronella_girondica"/>
<taxon idref="Crotalus_viridis"/>
<taxon idref="D_unicolo"/>
<taxon idref="Demansia_atra"/>
<taxon idref="Dendroaspis_polylepis"/>
<taxon idref="Dipsina_multimaculata"/>
<taxon idref="Dispholidus_typus"/>
<taxon idref="Ditypophis_vivax"/>
<taxon idref="Duberria_lutrix"/>
<taxon idref="EBG1363"/>
<taxon idref="EBG2607"/>
<taxon idref="EBG2610"/>
<taxon idref="EBG2673"/>
<taxon idref="EI_138"/>
<taxon idref="EI_166"/>
<taxon idref="EI_72"/>
<taxon idref="ELI373"/>
<taxon idref="ELI509"/>
<taxon idref="ELI510"/>
<taxon idref="ELIPEMR18"/>
<taxon idref="E_auro"/>
<taxon idref="FFNR002"/>
<taxon idref="Grayia_tholloni"/>
<taxon idref="HB282"/>
<taxon idref="Hemorrhois_hippocrepis"/>
<taxon idref="Hemorrhois_ravergieri"/>
<taxon idref="Hypsiglena_torquata"/>
<taxon idref="JM01442"/>
<taxon idref="Lycodon"/>
<taxon idref="Lycophidion_capense"/>
<taxon idref="MBUR03179"/>
<taxon idref="MBUR03481"/>
<taxon idref="MBUR08097"/>
<taxon idref="MBUR08206"/>
<taxon idref="MBUR8574"/>
<taxon idref="MOZ14_298"/>
<taxon idref="MTSN10482"/>
<taxon idref="MTSN7300"/>
<taxon idref="MTSN7373"/>
<taxon idref="MTSN8200"/>
<taxon idref="Madagascarophis_colubrinus"/>
<taxon idref="Micrelaps_bicoloratus"/>
<taxon idref="Naja_kaouthia"/>
<taxon idref="Naja_multifasciata"/>
<taxon idref="Naja_nivea"/>
<taxon idref="Natrix_natrix"/>
<taxon idref="Ophiophagus_hannah"/>
<taxon idref="Oxyrhabdium_leporinum"/>
<taxon idref="Platyceps_florulentus"/>
<taxon idref="Psammodynastes_pulverulentus"/>
<taxon idref="Psammophis"/>
<taxon idref="Pseudaspis_cana"/>
<taxon idref="Ptyas_mucosus"/>
<taxon idref="Rhamphiophis_rostratus"/>
<taxon idref="SPN091"/>
<taxon idref="TGET1-67"/>
<taxon idref="T_sem"/>
<taxon idref="Thamnophis_sirtalis"/>
<taxon idref="Thom605"/>
<taxon idref="Thom637"/>
<taxon idref="Tyr01"/>
<taxon idref="WC-ANG001"/>
<taxon idref="WC12-A082"/>
<taxon idref="WC12-A109"/>
<taxon idref="WC12_A136"/>
<taxon idref="WC3903"/>
<taxon idref="WCDNA0087"/>
<taxon idref="WCDNA816"/>
<taxon idref="WRB933"/>
<taxon idref="Walterinnesia_aegyptia"/>
<taxon idref="jes567"/>
<taxon idref="jes592"/>
<taxon idref="jes621"/>
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<LogNormal id="LogNormalDistributionModel.03" name="distr" offset="3.87">
<parameter id="RealParameter.025" estimate="false" name="M">3.6</parameter>
<parameter id="RealParameter.026" estimate="false" lower="0.0" name="S" upper="5.0">0.095</parameter>
</LogNormal>
</distribution>
<distribution id="c6.prior" spec="beast.math.distributions.MRCAPrior" monophyletic="true" tree="@Tree.t:ck-hme-reducedCYTB">
<taxonset id="c6" spec="TaxonSet">
<taxon idref="631120"/>
<taxon idref="631245"/>
<taxon idref="759"/>
<taxon idref="Afronatrix_anscopus"/>
<taxon idref="Agkistrodon_piscivorus"/>
<taxon idref="Alsophis_portoricensis"/>
<taxon idref="Amblyodipsas_dimidiata"/>
<taxon idref="Amplorhinus_multimaculatus_PEM"/>
<taxon idref="Aspidelaps_scutatus"/>
<taxon idref="Atheris_nitschei"/>
<taxon idref="B_forst"/>
<taxon idref="Boiga_dendrophila"/>
<taxon idref="Buhoma_procterae"/>
<taxon idref="Bungarus_fasciatus"/>
<taxon idref="Calliophis_bivirgatus"/>
<taxon idref="Cemophora_coccinea"/>
<taxon idref="Coluber_dorri"/>
<taxon idref="Coronella_girondica"/>
<taxon idref="Crotalus_viridis"/>
<taxon idref="D_unicolo"/>
<taxon idref="Demansia_atra"/>
<taxon idref="Dendroaspis_polylepis"/>
<taxon idref="Dipsina_multimaculata"/>
<taxon idref="Dispholidus_typus"/>
<taxon idref="Ditypophis_vivax"/>
<taxon idref="Duberria_lutrix"/>
<taxon idref="EBG1363"/>
<taxon idref="EBG2607"/>
<taxon idref="EBG2610"/>
<taxon idref="EBG2673"/>
<taxon idref="EI_138"/>
<taxon idref="EI_166"/>
<taxon idref="EI_72"/>
<taxon idref="ELI373"/>
<taxon idref="ELI509"/>
<taxon idref="ELI510"/>
<taxon idref="ELIPEMR18"/>
<taxon idref="E_auro"/>
<taxon idref="FFNR002"/>
<taxon idref="Grayia_tholloni"/>
<taxon idref="HB282"/>
<taxon idref="Hemorrhois_hippocrepis"/>
<taxon idref="Hemorrhois_ravergieri"/>
<taxon idref="Hypsiglena_torquata"/>
<taxon idref="JM01442"/>
<taxon idref="Lycodon"/>
<taxon idref="Lycophidion_capense"/>
<taxon idref="MBUR03179"/>
<taxon idref="MBUR03481"/>
<taxon idref="MBUR08097"/>
<taxon idref="MBUR08206"/>
<taxon idref="MBUR8574"/>
<taxon idref="MOZ14_298"/>
<taxon idref="MTSN10482"/>
<taxon idref="MTSN7300"/>
<taxon idref="MTSN7373"/>
<taxon idref="MTSN8200"/>
<taxon idref="Madagascarophis_colubrinus"/>
<taxon idref="Micrelaps_bicoloratus"/>
<taxon idref="Naja_kaouthia"/>
<taxon idref="Naja_multifasciata"/>
<taxon idref="Naja_nivea"/>
<taxon idref="Natrix_natrix"/>
<taxon idref="Ophiophagus_hannah"/>
<taxon idref="Oxyrhabdium_leporinum"/>
<taxon idref="Platyceps_florulentus"/>
<taxon idref="Psammodynastes_pulverulentus"/>
<taxon idref="Psammophis"/>
<taxon idref="Pseudaspis_cana"/>
<taxon idref="Ptyas_mucosus"/>
<taxon idref="Rhamphiophis_rostratus"/>
<taxon idref="SPN091"/>
<taxon idref="TGET1-67"/>
<taxon idref="T_sem"/>
<taxon idref="Thamnophis_sirtalis"/>
<taxon idref="Thom605"/>
<taxon idref="Thom637"/>
<taxon idref="Tyr01"/>
<taxon idref="WC-ANG001"/>
<taxon idref="WC12-A082"/>
<taxon idref="WC12-A109"/>
<taxon idref="WC12_A136"/>
<taxon idref="WC3903"/>
<taxon idref="WCDNA0087"/>
<taxon idref="WCDNA816"/>
<taxon idref="WRB933"/>
<taxon idref="Walterinnesia_aegyptia"/>
<taxon idref="jes567"/>
<taxon idref="jes592"/>
<taxon idref="jes621"/>
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<parameter id="RealParameter.027" estimate="false" name="M">3.47</parameter>
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</LogNormal>
</distribution>
<distribution id="c7.prior" spec="beast.math.distributions.MRCAPrior" monophyletic="true" tree="@Tree.t:ck-hme-reducedCYTB">
<taxonset id="c7" spec="TaxonSet">
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<taxon idref="Naja_multifasciata"/>
<taxon idref="Naja_nivea"/>
</taxonset>
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</LogNormal>
</distribution>
</distribution>
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</substModel>
</siteModel>
<branchRateModel id="RelaxedClock.c:ck-hme-reducedCYTB" spec="beast.evolution.branchratemodel.UCRelaxedClockModel" rateCategories="@rateCategories.c:ck-hme-reducedCYTB" tree="@Tree.t:ck-hme-reducedCYTB">
<LogNormal id="LogNormalDistributionModel.c:ck-hme-reducedCYTB" S="@ucldStdev.c:ck-hme-reducedCYTB" meanInRealSpace="true" name="distr">
<parameter id="RealParameter.01911" estimate="false" lower="0.0" name="M" upper="1.0">1.0</parameter>
</LogNormal>
<parameter id="ucldMean.c:ck-hme-reducedCYTB" estimate="false" name="clock.rate">1.0</parameter>
</branchRateModel>
</distribution>
<distribution id="treeLikelihood.ck-hme-reducedCMOS4" spec="TreeLikelihood" tree="@Tree.t:ck-hme-reducedCYTB">
<data idref="ck-hme-reducedCMOS4"/>
<siteModel id="SiteModel.s:ck-hme-reducedCMOS4" spec="SiteModel" gammaCategoryCount="4" mutationRate="@mutationRate.s:ck-hme-reducedCMOS4" shape="@gammaShape.s:ck-hme-reducedCMOS4">
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</substModel>
</siteModel>
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</LogNormal>
<parameter id="ucldMean.c:ck-hme-reducedCMOS4" estimate="false" name="clock.rate">0.1</parameter>
</branchRateModel>
</distribution>
<distribution id="treeLikelihood.ck-hme-reducedND4" spec="TreeLikelihood" tree="@Tree.t:ck-hme-reducedCYTB">
<data idref="ck-hme-reducedND4"/>
<siteModel id="SiteModel.s:ck-hme-reducedND4" spec="SiteModel" gammaCategoryCount="4" mutationRate="@mutationRate.s:ck-hme-reducedND4" shape="@gammaShape.s:ck-hme-reducedND4">
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<frequencies id="freqs.s:ck-hme-reducedND4" spec="Frequencies" data="@ck-hme-reducedND4"/>
</substModel>
</siteModel>
<branchRateModel id="RelaxedClock.c:ck-hme-reducedND4" spec="beast.evolution.branchratemodel.UCRelaxedClockModel" rateCategories="@rateCategories.c:ck-hme-reducedND4" tree="@Tree.t:ck-hme-reducedCYTB">
<LogNormal id="LogNormalDistributionModel.c:ck-hme-reducedND4" S="@ucldStdev.c:ck-hme-reducedND4" meanInRealSpace="true" name="distr">
<parameter id="RealParameter.0211" estimate="false" lower="0.0" name="M" upper="1.0">1.0</parameter>
</LogNormal>
<parameter id="ucldMean.c:ck-hme-reducedND4" estimate="false" name="clock.rate">1.0</parameter>
</branchRateModel>
</distribution>
</distribution>
</distribution>
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<operator id="RBratescaler.s:ck-hme-reducedCYTB" spec="RBScaleOperator" count="@RBcount.s:ck-hme-reducedCYTB" parameter="@RBrates.s:ck-hme-reducedCYTB" scaleFactor="0.5" weight="1.0"/>
<operator id="RBOperator.s:ck-hme-reducedCMOS4" spec="RBOperator" count="@RBcount.s:ck-hme-reducedCMOS4" rates="@RBrates.s:ck-hme-reducedCMOS4" weight="1.0"/>
<operator id="RBratescaler.s:ck-hme-reducedCMOS4" spec="RBScaleOperator" count="@RBcount.s:ck-hme-reducedCMOS4" parameter="@RBrates.s:ck-hme-reducedCMOS4" scaleFactor="0.5" weight="1.0"/>
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<operator id="mutationRateScaler.s:ck-hme-reducedCMOS4" spec="ScaleOperator" parameter="@mutationRate.s:ck-hme-reducedCMOS4" scaleFactor="0.5" weight="0.1"/>
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<operator id="CategoriesRandomWalk.c:ck-hme-reducedCYTB" spec="IntRandomWalkOperator" parameter="@rateCategories.c:ck-hme-reducedCYTB" weight="10.0" windowSize="1"/>
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<operator id="ucldStdevScaler.c:ck-hme-reducedCMOS4" spec="ScaleOperator" parameter="@ucldStdev.c:ck-hme-reducedCMOS4" scaleFactor="0.5" weight="3.0"/>
<operator id="CategoriesRandomWalk.c:ck-hme-reducedCMOS4" spec="IntRandomWalkOperator" parameter="@rateCategories.c:ck-hme-reducedCMOS4" weight="10.0" windowSize="1"/>
<operator id="CategoriesSwapOperator.c:ck-hme-reducedCMOS4" spec="SwapOperator" intparameter="@rateCategories.c:ck-hme-reducedCMOS4" weight="10.0"/>
<operator id="CategoriesUniform.c:ck-hme-reducedCMOS4" spec="UniformOperator" parameter="@rateCategories.c:ck-hme-reducedCMOS4" weight="10.0"/>
<operator id="ucldStdevScaler.c:ck-hme-reducedND4" spec="ScaleOperator" parameter="@ucldStdev.c:ck-hme-reducedND4" scaleFactor="0.5" weight="3.0"/>
<operator id="CategoriesRandomWalk.c:ck-hme-reducedND4" spec="IntRandomWalkOperator" parameter="@rateCategories.c:ck-hme-reducedND4" weight="10.0" windowSize="1"/>
<operator id="CategoriesSwapOperator.c:ck-hme-reducedND4" spec="SwapOperator" intparameter="@rateCategories.c:ck-hme-reducedND4" weight="10.0"/>
<operator id="CategoriesUniform.c:ck-hme-reducedND4" spec="UniformOperator" parameter="@rateCategories.c:ck-hme-reducedND4" weight="10.0"/>
<operator id="YuleBirthRateScaler.t:ck-hme-reducedCYTB" spec="ScaleOperator" parameter="@birthRate.t:ck-hme-reducedCYTB" scaleFactor="0.75" weight="3.0"/>
<operator id="YuleModelTreeScaler.t:ck-hme-reducedCYTB" spec="ScaleOperator" scaleFactor="0.5" tree="@Tree.t:ck-hme-reducedCYTB" weight="3.0"/>
<operator id="YuleModelTreeRootScaler.t:ck-hme-reducedCYTB" spec="ScaleOperator" rootOnly="true" scaleFactor="0.5" tree="@Tree.t:ck-hme-reducedCYTB" weight="3.0"/>
<operator id="YuleModelUniformOperator.t:ck-hme-reducedCYTB" spec="Uniform" tree="@Tree.t:ck-hme-reducedCYTB" weight="30.0"/>
<operator id="YuleModelSubtreeSlide.t:ck-hme-reducedCYTB" spec="SubtreeSlide" tree="@Tree.t:ck-hme-reducedCYTB" weight="0.0"/>
<operator id="YuleModelNarrow.t:ck-hme-reducedCYTB" spec="Exchange" tree="@Tree.t:ck-hme-reducedCYTB" weight="0.0"/>
<operator id="YuleModelWide.t:ck-hme-reducedCYTB" spec="Exchange" isNarrow="false" tree="@Tree.t:ck-hme-reducedCYTB" weight="0.0"/>
<operator id="YuleModelWilsonBalding.t:ck-hme-reducedCYTB" spec="WilsonBalding" tree="@Tree.t:ck-hme-reducedCYTB" weight="0.0"/>
<logger id="tracelog" fileName="ck-hme-reducedCYTB.log" logEvery="100000" model="@posterior" sanitiseHeaders="true" sort="smart">
<log idref="posterior"/>
<log idref="likelihood"/>
<log idref="prior"/>
<log idref="treeLikelihood.ck-hme-reducedCMOS4"/>
<log idref="treeLikelihood.ck-hme-reducedCYTB"/>
<log id="TreeHeight.t:ck-hme-reducedCYTB" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:ck-hme-reducedCYTB"/>
<log idref="treeLikelihood.ck-hme-reducedND4"/>
<log idref="RBcount.s:ck-hme-reducedCYTB"/>
<log idref="RBrates.s:ck-hme-reducedCYTB"/>
<log idref="RBcount.s:ck-hme-reducedCMOS4"/>
<log idref="RBrates.s:ck-hme-reducedCMOS4"/>
<log idref="RBcount.s:ck-hme-reducedND4"/>
<log idref="RBrates.s:ck-hme-reducedND4"/>
<log idref="mutationRate.s:ck-hme-reducedCYTB"/>
<log idref="gammaShape.s:ck-hme-reducedCYTB"/>
<log idref="mutationRate.s:ck-hme-reducedCMOS4"/>
<log idref="gammaShape.s:ck-hme-reducedCMOS4"/>
<log idref="mutationRate.s:ck-hme-reducedND4"/>
<log idref="gammaShape.s:ck-hme-reducedND4"/>
<log idref="ucldStdev.c:ck-hme-reducedCYTB"/>
<log id="rate.c:ck-hme-reducedCYTB" spec="beast.evolution.branchratemodel.RateStatistic" branchratemodel="@RelaxedClock.c:ck-hme-reducedCYTB" tree="@Tree.t:ck-hme-reducedCYTB"/>
<log idref="ucldStdev.c:ck-hme-reducedCMOS4"/>
<log id="rate.c:ck-hme-reducedCMOS4" spec="beast.evolution.branchratemodel.RateStatistic" branchratemodel="@RelaxedClock.c:ck-hme-reducedCMOS4" tree="@Tree.t:ck-hme-reducedCYTB"/>
<log idref="ucldStdev.c:ck-hme-reducedND4"/>
<log id="rate.c:ck-hme-reducedND4" spec="beast.evolution.branchratemodel.RateStatistic" branchratemodel="@RelaxedClock.c:ck-hme-reducedND4" tree="@Tree.t:ck-hme-reducedCYTB"/>
<log idref="YuleModel.t:ck-hme-reducedCYTB"/>
<log idref="birthRate.t:ck-hme-reducedCYTB"/>
<log idref="c1.prior"/>
<log idref="c2.prior"/>
<log idref="c3.prior"/>
<log idref="c4.prior"/>
<log idref="c5.prior"/>
<log idref="c6.prior"/>
<log idref="c7.prior"/>
</logger>
<logger id="screenlog" logEvery="100000">
<log idref="posterior"/>
<log id="ESS.0" spec="util.ESS" arg="@posterior"/>
<log idref="likelihood"/>
<log idref="prior"/>
</logger>
<logger id="treelog.t:ck-hme-reducedCYTB" fileName="$(tree).trees" logEvery="100000" mode="tree">
<log id="TreeWithMetaDataLogger.t:ck-hme-reducedCYTB" spec="beast.evolution.tree.TreeWithMetaDataLogger" branchratemodel="@RelaxedClock.c:ck-hme-reducedCYTB" tree="@Tree.t:ck-hme-reducedCYTB"/>
</logger>
</run>
</beast>
Thank you
hanlie engelbrecht
Dec 20, 2016, 9:21:11 AM12/20/16
to beast...@googlegroups.com
My apologies I copied from the wrong file...
So here we go
<parameter id="mutationRate.s:ck-hme-reducedCMOS4" name="stateNode">1.0</parameter>
<parameter id="gammaShape.s:ck-hme-reducedCMOS4" name="stateNode">1.0</parameter>
<parameter id="mutationRate.s:ck-hme-reducedND4" name="stateNode">1.0</parameter>
<parameter id="gammaShape.s:ck-hme-reducedND4" name="stateNode">1.0</parameter>
<parameter id="ucldStdev.c:ck-hme-reducedCYTB" lower="0.0" name="stateNode">0.1</parameter>
<stateNode id="rateCategories.c:ck-hme-reducedCYTB" spec="parameter.IntegerParameter" dimension="196">1</stateNode>
<parameter id="ucldStdev.c:ck-hme-reducedCMOS4" lower="0.0" name="stateNode">0.1</parameter>
<stateNode id="rateCategories.c:ck-hme-reducedCMOS4" spec="parameter.IntegerParameter" dimension="196">1</stateNode>
<parameter id="ucldStdev.c:ck-hme-reducedND4" lower="0.0" name="stateNode">0.1</parameter>
<stateNode id="rateCategories.c:ck-hme-reducedND4" spec="parameter.IntegerParameter" dimension="196">1</stateNode>
<parameter id="birthRate.t:ck-hme-reducedCYTB" name="stateNode">1.0</parameter>
</state>
<init spec="beast.util.TreeParser" id="StartingTree.t:xyz" IsLabelledNewick="true">
<input name="newick">(Gekko_gekko:0.31902879128232,(((Cordylus_warreni:0.44867999832323724,Mabuya_longicaudata:0.391935480957059):0.04794422927649877,(Lacerta_viridis:0.7684266256364884,(Shinisaurus_crocodilarius:0.1495940640795923,Varanus_salvator:0.5454012920272993):0.175397386801603):0.04708843700918941):0.09804248943101634,(Ramphotyphlops_braminus:0.5992534120756248,(Boa_constrictor:0.1691477843777598,(Acrochordus_granulatus:0.3441562542156482,((Atheris_nitschei:0.1627944218840307,(Agkistrodon_piscivorus:0.0758771066318411,Crotalus_viridis:0.1107335804289542):0.04642628773161239):0.04803500652850756,(((Buhoma_procterae:0.16281358354069497,Micrelaps_bicoloratus:0.13008641705671287):0.028458516651071797,((Oxyrhabdium_leporinum:0.20789196853086467,(Calliophis_bivirgatus:0.19961033330966105,((Ophiophagus_hannah:0.09022637425307845,Dendroaspis_polylepis:0.12819277854046418):0.02273934152385082,(Bungarus_fasciatus:0.17180730955793733,((Walterinnesia_aegyptia:0.09373634988404334,Aspidelaps_scutatus:0.14634917205862852):0.012493939413686483,(Naja_kaouthia:0.07271124876261492,(Naja_nivea:0.08453957539453061,Naja_multifasciata:0.07358694199340188):0.011008116450684335):0.02308045904087419):0.007211370883834167):0.01081830717080745):0.01498666738355503):0.01863820196172772):0.01289017914417534,((Lycophidion_capense:0.1989254958294404,(Psammodynastes_pulverulentus:0.1651611896625802,Amblyodipsas_dimidiata:0.08167281568204432):0.022604588839760575):0.017034584314087775,(Pseudaspis_cana:0.11039268942209479,((Rhamphiophis_rostratus:0.12266560508102575,(Dipsina_multimaculata:0.09839774526044831,Psammophis:0.11001953990867697):0.017326291411537742):0.04571379010744736,(Ditypophis_vivax:0.10989320204061115,(Madagascarophis_colubrinus:0.145292399663282,(Amplorhinus_multimaculatus_PEM:0.108818450087947,Duberria_lutrix:0.14942434077968159):0.026739853777421496):1.1585571542127582E-6):0.02159012158971274):0.011552935174124812):0.0061117614981720525):0.00716039352088238):0.0026694386553367533):0.029670301727059645,(((Alsophis_portoricensis:0.15767288339999475,Hypsiglena_torquata:0.11640335721490591):0.02265918467896033,(Grayia_tholloni:0.16088351136454015,(Afronatrix_anscopus:0.12065861673566602,(Natrix_natrix:0.11119419804373343,Thamnophis_sirtalis:0.10078655734865394):0.047077053735178565):0.02721621105960148):0.009252122531610896):0.012454741719293061,((Ptyas_mucosus:0.11323280691654758,(((E_auro:0.09213047752100145,Coluber_dorri:0.1039700738818723):0.008239835349921565,(Platyceps_florulentus:0.1300118072900145,(Hemorrhois_ravergieri:0.05437699360173065,Hemorrhois_hippocrepis:0.0662696469353441):0.019341498217411157):0.023300725051789595):0.018322240158085146,((Boiga_dendrophila:0.11086915082790227,B_forst:0.08740259483396429):0.06516575829601656,(T_sem:0.18051610623421466,(D_unicolo:0.13180554180665616,(WC3903:0.1235110098357437,(MTSN7300:0.09909031565335513,((Thom605:0.07678681610973581,(631245:0.049211221217251744,631120:0.040388353939587285):0.06709252777382613):0.03720199241810396,((FFNR002:0.026683498589464616,(ELIPEMR18:0.024402295551943176,(TGET1-67:0.010959094388633295,EI_72:0.01602181634566402):0.01874787776046949):0.008242751874496523):0.0036324074986255894,(JM01442:0.029096467878046095,(WC-ANG001:0.02405250716491425,(WRB933:0.021527331496343782,((WC12-A082:0.01564517378184549,WC12-A109:0.03219922813645959):8.25813907698425E-4,(Thom637:0.01416632743374846,MBUR8574:0.018126263529177233):0.021400005397132604):0.00408754361405439):0.0032379533035422625):0.010514585554111333):0.001959708854790021):0.05773752169753288):0.012668697487179692):0.01906230423050781):0.02563805174599465):0.027401082448186287):0.006445387272250747):0.007572904560991134):0.005022746717512794):0.004410371151304826,(Lycodon:0.1889098514783054,((Cemophora_coccinea:0.09808068007653281,Coronella_girondica:0.06601902034349227):0.04014414029333069,((ELI509:0.08025742728700402,(ELI373:0.075360440750885,(Dispholidus_typus:0.03117098171210797,EBG2673:0.0498062321835524):0.06537355462076477):0.029482528005488007):0.018204521011693897,((EBG2607:0.08826634386968002,(EBG2610:0.07248467716607965,jes592:0.05312032603922523):0.019732954973130212):0.019848798673544277,(((MTSN8200:0.07222121812706983,MOZ14_298:0.10997169008447494):0.01981624282937089,((MBUR03481:0.03230516840007325,EBG1363:0.03178156237025909):0.044006329898455876,(MTSN7373:0.06650371272623024,MBUR08206:0.10021557995770136):0.014853100722340917):0.013413305240862039):0.010985707898862218,((Tyr01:0.04895990401078221,(WCDNA816:0.009332706070468877,WCDNA0087:0.008248936342889035):0.026676301757393217):0.051500933951269756,((WC12_A136:0.07680240304376107,(jes567:0.044740961652251166,(MBUR08097:0.02084149779280331,jes621:0.03247765237492084):0.021234835357484938):0.046377020089459986):0.01883892202559001,(HB282:0.07012338293777676,(SPN091:0.0824991658590577,((759:0.03822695423357492,EI_138:0.054183997611483736):0.0055924789199954805,((MTSN10482:0.02794057253196547,EI_166:0.025609712252023353):0.024395827194686026,(MBUR03179:0.02975877024958118,ELI510:0.0440528653902208):0.010615670678545408):0.015557005744584407):0.015468679888270609):0.013190500897640955):0.006826980767654867):0.006382761677202753):0.010679384879918485):0.0313399870219242):0.01821619929922269):0.013488593976405339):0.0055393968067707355):0.0026324861699162927):0.03485986133308194):0.015720386871647563):0.024716794119523433):0.06868069104039631):0.028540288421351034):0.2862157885554244):0.2653191071502857):0.31902879128231987);</input>
<distribution id="c1.prior" spec="beast.math.distributions.MRCAPrior" monophyletic="false" tree="@Tree.t:ck-hme-reducedCYTB">
<Uniform id="Uniform.0" lower="156.0" name="distr" upper="248.0"/>
</distribution>
<distribution id="c2.prior" spec="beast.math.distributions.MRCAPrior" monophyletic="false" tree="@Tree.t:ck-hme-reducedCYTB">
<LogNormal id="LogNormalDistributionModel.01" name="distr" offset="5.25">
<parameter id="RealParameter.019" estimate="false" name="M">5.105</parameter>
<parameter id="RealParameter.020" estimate="false" lower="0.0" name="S" upper="5.0">0.059</parameter>
</LogNormal>
</distribution>
<distribution id="c3.prior" spec="beast.math.distributions.MRCAPrior" monophyletic="false" tree="@Tree.t:ck-hme-reducedCYTB">
<taxonset id="c3" spec="TaxonSet">
<taxon idref="Varanus_salvator"/>
<taxon idref="Shinisaurus_crocodilarius"/>
</taxonset>
<LogNormal id="LogNormalDistributionModel.011" name="distr" offset="4.65">
<parameter id="RealParameter.021" estimate="false" name="M">4.44</parameter>
<parameter id="RealParameter.022" estimate="false" lower="0.0" name="S" upper="5.0">0.08</parameter>
</LogNormal>
</distribution>
<distribution id="c4.prior" spec="beast.math.distributions.MRCAPrior" monophyletic="false" tree="@Tree.t:ck-hme-reducedCYTB">
<distribution id="c5.prior" spec="beast.math.distributions.MRCAPrior" monophyletic="false" tree="@Tree.t:ck-hme-reducedCYTB">
<distribution id="c6.prior" spec="beast.math.distributions.MRCAPrior" monophyletic="false" tree="@Tree.t:ck-hme-reducedCYTB">
<distribution id="c7.prior" spec="beast.math.distributions.MRCAPrior" monophyletic="false" tree="@Tree.t:ck-hme-reducedCYTB">
<taxonset id="c7" spec="TaxonSet">
<taxon idref="Naja_kaouthia"/>
<taxon idref="Naja_multifasciata"/>
<taxon idref="Naja_nivea"/>
</taxonset>
<LogNormal id="LogNormalDistributionModel.05" name="distr" offset="2.99">
<parameter id="RealParameter.029" estimate="false" name="M">2.595</parameter>
<parameter id="RealParameter.030" estimate="false" lower="0.0" name="S" upper="5.0">0.099</parameter>
</LogNormal>
</distribution>
</distribution>
<distribution id="likelihood" spec="util.CompoundDistribution">
<distribution id="treeLikelihood.ck-hme-reducedCYTB" spec="TreeLikelihood" data="@ck-hme-reducedCYTB" tree="@Tree.t:ck-hme-reducedCYTB">
<siteModel id="SiteModel.s:ck-hme-reducedCYTB" spec="SiteModel" gammaCategoryCount="4" mutationRate="@mutationRate.s:ck-hme-reducedCYTB" shape="@gammaShape.s:ck-hme-reducedCYTB">
<parameter id="proportionInvariant.s:ck-hme-reducedCYTB" estimate="false" lower="0.0" name="proportionInvariant" upper="1.0">0.0</parameter>
<substModel id="RB.s:ck-hme-reducedCYTB" spec="RB" count="@RBcount.s:ck-hme-reducedCYTB" rates="@RBrates.s:ck-hme-reducedCYTB">
<frequencies id="freqs.s:ck-hme-reducedCYTB" spec="Frequencies" data="@ck-hme-reducedCYTB"/>
</substModel>
</siteModel>
<branchRateModel id="RelaxedClock.c:ck-hme-reducedCYTB" spec="beast.evolution.branchratemodel.UCRelaxedClockModel" rateCategories="@rateCategories.c:ck-hme-reducedCYTB" tree="@Tree.t:ck-hme-reducedCYTB">
<LogNormal id="LogNormalDistributionModel.c:ck-hme-reducedCYTB" S="@ucldStdev.c:ck-hme-reducedCYTB" meanInRealSpace="true" name="distr">
<parameter id="RealParameter.0191" estimate="false" lower="0.0" name="M" upper="1.0">1.0</parameter>
</LogNormal>
<parameter id="ucldMean.c:ck-hme-reducedCYTB" estimate="false" name="clock.rate">1.0</parameter>
</branchRateModel>
</distribution>
<distribution id="treeLikelihood.ck-hme-reducedCMOS4" spec="TreeLikelihood" tree="@Tree.t:ck-hme-reducedCYTB">
<data idref="ck-hme-reducedCMOS4"/>
<siteModel id="SiteModel.s:ck-hme-reducedCMOS4" spec="SiteModel" gammaCategoryCount="4" mutationRate="@mutationRate.s:ck-hme-reducedCMOS4" shape="@gammaShape.s:ck-hme-reducedCMOS4">
<parameter id="proportionInvariant.s:ck-hme-reducedCMOS4" estimate="false" lower="0.0" name="proportionInvariant" upper="1.0">0.0</parameter>
<substModel id="RB.s:ck-hme-reducedCMOS4" spec="RB" count="@RBcount.s:ck-hme-reducedCMOS4" rates="@RBrates.s:ck-hme-reducedCMOS4">
<frequencies id="freqs.s:ck-hme-reducedCMOS4" spec="Frequencies" data="@ck-hme-reducedCMOS4"/>
</substModel>
</siteModel>
<branchRateModel id="RelaxedClock.c:ck-hme-reducedCMOS4" spec="beast.evolution.branchratemodel.UCRelaxedClockModel" rateCategories="@rateCategories.c:ck-hme-reducedCMOS4" tree="@Tree.t:ck-hme-reducedCYTB">
<LogNormal id="LogNormalDistributionModel.c:ck-hme-reducedCMOS4" S="@ucldStdev.c:ck-hme-reducedCMOS4" meanInRealSpace="true" name="distr">
<parameter id="RealParameter.0201" estimate="false" lower="0.0" name="M" upper="1.0">1.0</parameter>
<operator id="mutationRateScaler.s:ck-hme-reducedCYTB" spec="ScaleOperator" parameter="@mutationRate.s:ck-hme-reducedCYTB" scaleFactor="0.5" weight="0.1"/>
<operator id="gammaShapeScaler.s:ck-hme-reducedCYTB" spec="ScaleOperator" parameter="@gammaShape.s:ck-hme-reducedCYTB" scaleFactor="0.5" weight="0.1"/>
<operator id="mutationRateScaler.s:ck-hme-reducedCMOS4" spec="ScaleOperator" parameter="@mutationRate.s:ck-hme-reducedCMOS4" scaleFactor="0.5" weight="0.1"/>
<operator id="gammaShapeScaler.s:ck-hme-reducedCMOS4" spec="ScaleOperator" parameter="@gammaShape.s:ck-hme-reducedCMOS4" scaleFactor="0.5" weight="0.1"/>
<operator id="mutationRateScaler.s:ck-hme-reducedND4" spec="ScaleOperator" parameter="@mutationRate.s:ck-hme-reducedND4" scaleFactor="0.5" weight="0.1"/>
<log idref="c1"/>
<log idref="c2.prior"/>
<log idref="c3.prior"/>
<log idref="c4.prior"/>
<log idref="c5.prior"/>
<log idref="c6.prior"/>
<log idref="c7.prior"/>
</logger>
<logger id="screenlog" logEvery="100000">
<log idref="posterior"/>
<log id="ESS.0" spec="util.ESS" arg="@posterior"/>
<log idref="likelihood"/>
<log idref="prior"/>
</logger>
<logger id="treelog.t:ck-hme-reducedCYTB" fileName="$(tree).trees" logEvery="100000" mode="tree">
<log id="TreeWithMetaDataLogger.t:ck-hme-reducedCYTB" spec="beast.evolution.tree.TreeWithMetaDataLogger" branchratemodel="@RelaxedClock.c:ck-hme-reducedCYTB" tree="@Tree.t:ck-hme-reducedCYTB"/>
</logger>
</run>
</beast>
Thank you!
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Hanlie M. Engelbrecht (PhD Candidate)
Biodiversity Research Information Monitoring
South African National Biodiversity Institute (SANBI)
P/Bag X7, Claremont, 7735
Cape Town
South Africa
Contact info: H.Enge...@sanbi.org.za /+27217998749/+27828753492
Biodiversity Research Information Monitoring
South African National Biodiversity Institute (SANBI)
P/Bag X7, Claremont, 7735
Cape Town
South Africa
Contact info: H.Enge...@sanbi.org.za /+27217998749/+27828753492
Remco Bouckaert
Dec 20, 2016, 12:47:10 PM12/20/16
to beast...@googlegroups.com
Hi Hanlie,
This log entry is problematic :
> <log idref="c1"/>
and should be
<log idref=“c1.prior"/>
The first one refers to the taxon set, while the second to the MRCA prior.
Cheers,
Remco
This log entry is problematic :
> <log idref="c1"/>
and should be
<log idref=“c1.prior"/>
The first one refers to the taxon set, while the second to the MRCA prior.
Cheers,
Remco
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