*Beast taxon sets error
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jim h
Oct 18, 2014, 9:10:11 AM10/18/14
to beast...@googlegroups.com
Dear Beast Users,
I am trying to get a species tree for 4 species of Nothofagus from two datesets, a partitioned ITS sequence and a non-partitioned cpDNA sequence. The two datasets have the same number of sequences and they have the same names. I am having trouble with an error in *Beast which reads as follows:
Error 110 parsing the xml input file
validate and intialize error: Cannot find taxon 10NE1_cunninghamii1 in data
I do not have 10NE1_cunninghamii1 in my data but *Beast has named the
I have tried to fix this problem by using a trait file to assign each sequence to a species group. I have also tried the advice in this post https://groups.google.com/forum/#!searchin/beast-users/Cannot$20find$20taxon/beast-users/CcdWjtsxk-A/3k8eAW58C7gJ but am unable to edit the xml file correctly in Xm editor.
Are other people having trouble with assigning sequences to taxa in *Beast and how can I get around this problem?
I need help with this. Very frustrating!
Regards,
Jim
I am trying to get a species tree for 4 species of Nothofagus from two datesets, a partitioned ITS sequence and a non-partitioned cpDNA sequence. The two datasets have the same number of sequences and they have the same names. I am having trouble with an error in *Beast which reads as follows:
Error 110 parsing the xml input file
validate and intialize error: Cannot find taxon 10NE1_cunninghamii1 in data
I do not have 10NE1_cunninghamii1 in my data but *Beast has named the
I have tried to fix this problem by using a trait file to assign each sequence to a species group. I have also tried the advice in this post https://groups.google.com/forum/#!searchin/beast-users/Cannot$20find$20taxon/beast-users/CcdWjtsxk-A/3k8eAW58C7gJ but am unable to edit the xml file correctly in Xm editor.
Are other people having trouble with assigning sequences to taxa in *Beast and how can I get around this problem?
I need help with this. Very frustrating!
Regards,
Jim
Remco Bouckaert
Oct 19, 2014, 5:04:41 PM10/19/14
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Dear Jim,
Are you running Version 2.1.3? Can you send me the XML so I can have a look.
Cheers,
Remco
Are you running Version 2.1.3? Can you send me the XML so I can have a look.
Cheers,
Remco
Remco Bouckaert
Oct 20, 2014, 4:10:39 PM10/20/14
to beast...@googlegroups.com
Dear James,
The file you sent has a problem with the calibration id="Lophozonia.prior" where it uses IDs of taxa but add a one at the end. Since these taxa are already defined, just removing the 1 in all IDs leads to duplicate IDs, which is not allowed in XML. So, the file can be fixed by replacing all id with idref, remove the 1 and remove spec="Taxon".
For example,
<taxon id="10NE1_cunninghamii1" spec="Taxon"/>
becomes
<taxon idref="10NE1_cunninghamii"/>
This makes the file parse, but the StartBeastStartState, which initialises the gene and species trees, does not take these calibrations in account in this file (though normally, it does so this is something I will look into). So, I changed the XML to use another way of initialising the trees, which gives a less optimal starting state -- see attached.
Hope this helps,
Remco
The file you sent has a problem with the calibration id="Lophozonia.prior" where it uses IDs of taxa but add a one at the end. Since these taxa are already defined, just removing the 1 in all IDs leads to duplicate IDs, which is not allowed in XML. So, the file can be fixed by replacing all id with idref, remove the 1 and remove spec="Taxon".
For example,
<taxon id="10NE1_cunninghamii1" spec="Taxon"/>
becomes
<taxon idref="10NE1_cunninghamii"/>
This makes the file parse, but the StartBeastStartState, which initialises the gene and species trees, does not take these calibrations in account in this file (though normally, it does so this is something I will look into). So, I changed the XML to use another way of initialising the trees, which gives a less optimal starting state -- see attached.
Hope this helps,
Remco
jim h
Oct 20, 2014, 7:12:31 PM10/20/14
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Dear Remco,
Thanks for your help. I ran it and it works. However if I modify the xml file in Beauti (i simply changed the site models) it does not run again this time giving an error:
Thanks for your help. I ran it and it works. However if I modify the xml file in Beauti (i simply changed the site models) it does not run again this time giving an error:
Error 110 parsing the xml input file
validate and intialize error: Cannot find species for lineage 10NE1_cunninghamii
Error detected about here:
<beast>
<run id='mcmc' spec='MCMC'>
<distribution id='posterior' spec='util.CompoundDistribution'>
<distribution id='speciescoalescent' spec='util.CompoundDistribution'>
<distribution id='treePrior.t:ITS2' spec='beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution'>
Is this bug going to be fixed in Beauti 2? Do you know if other people are having trouble with the same issue and how do they get around it? I wonder if everyone modifies the xml file manually.
Regards,
James
Error detected about here:
<beast>
<run id='mcmc' spec='MCMC'>
<distribution id='posterior' spec='util.CompoundDistribution'>
<distribution id='speciescoalescent' spec='util.CompoundDistribution'>
<distribution id='treePrior.t:ITS2' spec='beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution'>
Is this bug going to be fixed in Beauti 2? Do you know if other people are having trouble with the same issue and how do they get around it? I wonder if everyone modifies the xml file manually.
Regards,
James
Remco Bouckaert
Oct 21, 2014, 2:45:34 AM10/21/14
to beast...@googlegroups.com
Dear James,
Once an XML file is edited using a text editor, there is no guarantee that BEAUti will be able to handle the tree, and all kinds of unexpected things can happen.
By the way, I passed your file to Joseph and he observed that you use the Yule prior for the species tree. This prior is not appropriate when there are calibrations. The StartBeastStartState object, which initialises the gene trees and species tree, does not recognise the calibrations with a Yule prior, but does so with a Calibrated Yule prior. This probably explains why the file you posted does not start even when taxa IDs are fixed.
Cheers,
Remco
Once an XML file is edited using a text editor, there is no guarantee that BEAUti will be able to handle the tree, and all kinds of unexpected things can happen.
By the way, I passed your file to Joseph and he observed that you use the Yule prior for the species tree. This prior is not appropriate when there are calibrations. The StartBeastStartState object, which initialises the gene trees and species tree, does not recognise the calibrations with a Yule prior, but does so with a Calibrated Yule prior. This probably explains why the file you posted does not start even when taxa IDs are fixed.
Cheers,
Remco
jim h
Oct 24, 2014, 12:29:27 AM10/24/14
to beast...@googlegroups.com
Thanks for that. My problems have not been solved with Starbeast. Even if I edit the xml file as you suggested I still get error messages. Almost given up with starbeast.
jim h
Oct 26, 2014, 8:29:15 PM10/26/14
to beast...@googlegroups.com
I followed your advice to modify the xml file. Now I get an error as below:
java.lang.Exception: Taxon not found in tree: NC10NE1_cunninghamii
at beast.evolution.speciation.CalibratedYuleModel.initAndValidate(Unknown Source)
at beast.util.XMLParser.initPlugins(Unknown Source)
at beast.util.XMLParser.parse(Unknown Source)
at beast.util.XMLParser.parseFile(Unknown Source)
at beast.app.BeastMCMC.parseArgs(Unknown Source)
at beast.app.beastapp.BeastMain.main(Unknown Source)
java.lang.Exception: Taxon not found in tree: NC10NE1_cunninghamii
at beast.evolution.speciation.CalibratedYuleModel.initAndValidate(Unknown Source)
at beast.util.XMLParser.initPlugins(Unknown Source)
at beast.util.XMLParser.parse(Unknown Source)
at beast.util.XMLParser.parseFile(Unknown Source)
at beast.app.BeastMCMC.parseArgs(Unknown Source)
at beast.app.beastapp.BeastMain.main(Unknown Source)
Error 110 parsing the xml input file
validate and intialize error: Taxon not found in tree: NC10NE1_cunninghamii
Error detected about here:
<beast>
<run id='mcmc' spec='MCMC'>
<distribution id='posterior' spec='util.CompoundDistribution'>
<distribution id='prior' spec='util.CompoundDistribution'>
<distribution id='CalibratedYuleModel.t:Species' spec='beast.evolution.speciation.CalibratedYuleModel'>
Is this problem going to be fixed? It is making starbeast unusable.
<distribution id='CalibratedYuleModel.t:Species' spec='beast.evolution.speciation.CalibratedYuleModel'>
Is this problem going to be fixed? It is making starbeast unusable.
Cymon
Nov 12, 2014, 11:44:37 AM11/12/14
to beast...@googlegroups.com
Hi Jim and Remco,
Maybe I an add to this...
I'm getting a similar error with Beast 2.1.3 and Beauti 2 using the *beast template:
java.lang.Exception: Cannot find species with name Chlorella_vulgaris in species tree
at beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution.initAndValidate(Unknown Source)
Maybe I an add to this...
I'm getting a similar error with Beast 2.1.3 and Beauti 2 using the *beast template:
java.lang.Exception: Cannot find species with name Chlorella_vulgaris in species tree
at beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution.initAndValidate(Unknown Source)
at beast.util.XMLParser.initPlugins(Unknown Source)
at beast.util.XMLParser.parse(Unknown Source)
at beast.util.XMLParser.parseFile(Unknown Source)
at beast.app.BeastMCMC.parseArgs(Unknown Source)
at beast.app.beastapp.BeastMain.main(Unknown Source)
Error 110 parsing the xml input file
validate and intialize error: Cannot find species with name Chlorella_vulgaris in species tree
Error detected about here:
<beast>
<run id='mcmc' spec='MCMC'>
<distribution id='posterior' spec='util.CompoundDistribution'>
<distribution id='speciescoalescent' spec='util.CompoundDistribution'>
<distribution id='treePrior.t:p2' spec='beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution'>
Data: 30 taxa (species) with names X_Y_Z where X is genus Y is species and Z is an arbitrary tail to distinguish lineages from species taxa, each species has one lineage/sequence:
Taxon elements look like this:
<taxonset id="taxonsuperset" spec="TaxonSet">
<taxon id="Nymphaea_alba" spec="TaxonSet">
<taxon id="Nymphaea_alba_A1" spec="Taxon"/>
</taxon>
etc.
5 data partitions p1-p5
1) using beauti load template, data, set taxon sets, save - > runs without error
2) load template, data, set taxon sets, and in CLOCK individually change (ie by clicking on the partitions p1-p5 in the left pane) each strict clock of each partition to a RelaxedLogNormal, save -> runs without error
3) now if I click on p1 again in the CLOCK tab and clone down from p1 to p2-p5, save data -> error:
java.lang.Exception: Cannot find species with name Chlorella_vulgaris in species tree
at beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution.initAndValidate(Unknown Source)
Data: 30 taxa (species) with names X_Y_Z where X is genus Y is species and Z is an arbitrary tail to distinguish lineages from species taxa, each species has one lineage/sequence:
Taxon elements look like this:
<taxonset id="taxonsuperset" spec="TaxonSet">
<taxon id="Nymphaea_alba" spec="TaxonSet">
<taxon id="Nymphaea_alba_A1" spec="Taxon"/>
</taxon>
etc.
5 data partitions p1-p5
1) using beauti load template, data, set taxon sets, save - > runs without error
2) load template, data, set taxon sets, and in CLOCK individually change (ie by clicking on the partitions p1-p5 in the left pane) each strict clock of each partition to a RelaxedLogNormal, save -> runs without error
3) now if I click on p1 again in the CLOCK tab and clone down from p1 to p2-p5, save data -> error:
java.lang.Exception: Cannot find species with name Chlorella_vulgaris in species tree
at beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution.initAndValidate(Unknown Source)
at beast.util.XMLParser.initPlugins(Unknown Source)
at beast.util.XMLParser.parse(Unknown Source)
at beast.util.XMLParser.parseFile(Unknown Source)
at beast.app.BeastMCMC.parseArgs(Unknown Source)
at beast.app.beastapp.BeastMain.main(Unknown Source)
Error 110 parsing the xml input file
validate and intialize error: Cannot find species with name Chlorella_vulgaris in species tree
Error detected about here:
<beast>
<run id='mcmc' spec='MCMC'>
<distribution id='posterior' spec='util.CompoundDistribution'>
<distribution id='speciescoalescent' spec='util.CompoundDistribution'>
<distribution id='treePrior.t:p2' spec='beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution'>
4) same thing occurs if I start-over and only try cloning the RelaxedLogNormal clock to from p1 to p2-p5:
On standard error I get this printed to the screen:
Processin: TreeHeight.t:p1
Processin: treeTopFinder
Processin: UniformOperator.t:p1
Processin: ucldStdevScaler.c:p1
Processin: ucldStdevPrior.c:p1
Processin: SBI
Processin: CategoriesSwapOperator.c:p1
Processin: ucldMean.c:p1
Processin: narrow.t:p1
Processin: treeScaler.t:p1
Processin: wide.t:p1
Processin: TreeWithMetaDataLogger.t:p1
Processin: RealParameter.0
Processin: RelaxedClock.c:p1
Processin: CategoriesRandomWalk.c:p1
Processin: ucldMeanScaler.c:p1
Processin: CategoriesUniform.c:p1
Processin: TaxonSet.p1
Processin: rate.c:p1
Processin: relaxedUpDownOperator.c:p1
Processin: LogNormalDistributionModel.c:p1
Processin: updown.p1
Processin: MeanRatePrior.c:p1
Processin: WilsonBalding.t:p1
Processin: RandomGeneTree.t:p1
Processin: rateCategories.c:p1
Processin: treePrior.t:p1
Processin: SubtreeSlide.t:p1
Processin: ucldStdev.c:p1
Processin: SpeciesTreeLoggerX
Processin: Reheight.t:Species
Processin: updown.all.Species
Processin: strictClockUpDownOperator.c:p1
Processin: treeRootScaler.t:p1
Cannot find species with name Chlorella_vulgaris in species treeCannot find species with name Chlorella_vulgaris in species treeCannot find species with name Chlorella_vulgaris in species treeCannot find species with name Chlorella_vulgaris in species treeCannot find species with name Chlorella_vulgaris in species treeCannot find species with name Chlorella_vulgaris in species treeCannot find species with name Chlorella_vulgaris in species treeCannot find species with name Chlorella_vulgaris in species treeCannot find species with name Chlorella_vulgaris in species treeCannot find species with name Chlorella_vulgaris in species treeProcessin: Tree.t:p1
etc for each partition.
This is the "diff" of the XML where each partition was individuallyset to RelaxedLogNormal (runs without error) versus the XML from when it was cloned down (runs with error):
I would have expected these to be identical yet that is clearly not the case, although some of this is obviously just trivially different placements of elements. The stuff in <distribution id="speciescoalescent" seems to be the issue but I cant figure out how to fix it:
[cymon@spiro run4]$ diff -ruN relaxedLogNormal.xml cloned2.xml
--- relaxedLogNormal.xml 2014-11-12 16:26:16.236002409 +0000
+++ cloned2.xml 2014-11-12 16:37:35.320026425 +0000
@@ -84,12 +84,12 @@
<taxon id="Chaetosphaeridium_globosum" spec="TaxonSet">
<taxon id="Chaetosphaeridium_globosum_H" spec="Taxon"/>
</taxon>
- <taxon id="Selaginella_moellendorffii" spec="TaxonSet">
- <taxon id="Selaginella_moellendorffii_S" spec="Taxon"/>
- </taxon>
<taxon id="Nephroselmis_olivacea" spec="TaxonSet">
<taxon id="Nephroselmis_olivacea_D" spec="Taxon"/>
</taxon>
+ <taxon id="Selaginella_moellendorffii" spec="TaxonSet">
+ <taxon id="Selaginella_moellendorffii_S" spec="Taxon"/>
+ </taxon>
<taxon id="Mesostigma_viride" spec="TaxonSet">
<taxon id="Mesostigma_viride_E" spec="Taxon"/>
</taxon>
@@ -154,55 +154,55 @@
</tree>
<parameter id="birthRate.t:Species" lower="0.0" name="stateNode" upper="10000.0">213.2021</parameter>
<parameter id="popMean" name="stateNode">1.0</parameter>
- <tree id="Tree.t:p3" name="stateNode">
- <taxonset id="TaxonSet.p3" spec="TaxonSet">
- <alignment filter="6106-11544" id="p3" spec="FilteredAlignment">
+ <tree id="Tree.t:p1" name="stateNode">
+ <taxonset id="TaxonSet.p1" spec="TaxonSet">
+ <alignment filter="1-2907" id="p1" spec="FilteredAlignment">
<data
idref="roya2_concat_30taxon_nucl_incl_5partitions"/>
</alignment>
</taxonset>
</tree>
- <tree id="Tree.t:p1" name="stateNode">
- <taxonset id="TaxonSet.p1" spec="TaxonSet">
- <alignment data="@roya2_concat_30taxon_nucl_incl_5partitions" filter="1-2907" id="p1" spec="FilteredAlignment"/>
- </taxonset>
- </tree>
+ <parameter id="ucldStdev.c:p1" lower="0.0" name="stateNode" upper="5.0">0.5</parameter>
+ <stateNode dimension="58" id="rateCategories.c:p1" spec="parameter.IntegerParameter">1</stateNode>
<tree id="Tree.t:p2" name="stateNode">
<taxonset id="TaxonSet.p2" spec="TaxonSet">
<alignment data="@roya2_concat_30taxon_nucl_incl_5partitions" filter="2908-6105" id="p2" spec="FilteredAlignment"/>
</taxonset>
</tree>
+ <stateNode dimension="58" id="rateCategories.c:p2" spec="parameter.IntegerParameter">1</stateNode>
+ <parameter id="ucldStdev.c:p2" lower="0.0" name="stateNode" upper="5.0">0.5</parameter>
+ <tree id="Tree.t:p3" name="stateNode">
+ <taxonset id="TaxonSet.p3" spec="TaxonSet">
+ <alignment data="@roya2_concat_30taxon_nucl_incl_5partitions" filter="6106-11544" id="p3" spec="FilteredAlignment"/>
+ </taxonset>
+ </tree>
+ <stateNode dimension="58" id="rateCategories.c:p3" spec="parameter.IntegerParameter">1</stateNode>
+ <parameter id="ucldStdev.c:p3" lower="0.0" name="stateNode" upper="5.0">0.5</parameter>
<tree id="Tree.t:p4" name="stateNode">
<taxonset id="TaxonSet.p4" spec="TaxonSet">
<alignment data="@roya2_concat_30taxon_nucl_incl_5partitions" filter="11545-13599" id="p4" spec="FilteredAlignment"/>
</taxonset>
</tree>
+ <stateNode dimension="58" id="rateCategories.c:p4" spec="parameter.IntegerParameter">1</stateNode>
+ <parameter id="ucldStdev.c:p4" lower="0.0" name="stateNode" upper="5.0">0.5</parameter>
<tree id="Tree.t:p5" name="stateNode">
<taxonset id="TaxonSet.p5" spec="TaxonSet">
<alignment data="@roya2_concat_30taxon_nucl_incl_5partitions" filter="13600-20100" id="p5" spec="FilteredAlignment"/>
</taxonset>
</tree>
- <parameter id="ucldStdev.c:p1" lower="0.0" name="stateNode" upper="5.0">0.5</parameter>
- <stateNode dimension="58" id="rateCategories.c:p1" spec="parameter.IntegerParameter">1</stateNode>
+ <stateNode dimension="58" id="rateCategories.c:p5" spec="parameter.IntegerParameter">1</stateNode>
+ <parameter id="ucldStdev.c:p5" lower="0.0" name="stateNode" upper="5.0">0.5</parameter>
+ <parameter id="ucldMean.c:p4" name="stateNode">1.0</parameter>
<parameter id="ucldMean.c:p2" name="stateNode">1.0</parameter>
- <parameter id="ucldStdev.c:p2" lower="0.0" name="stateNode" upper="5.0">0.5</parameter>
- <stateNode dimension="58" id="rateCategories.c:p2" spec="parameter.IntegerParameter">1</stateNode>
<parameter id="ucldMean.c:p3" name="stateNode">1.0</parameter>
- <parameter id="ucldStdev.c:p3" lower="0.0" name="stateNode" upper="5.0">0.5</parameter>
- <stateNode dimension="58" id="rateCategories.c:p3" spec="parameter.IntegerParameter">1</stateNode>
- <parameter id="ucldMean.c:p4" name="stateNode">1.0</parameter>
- <parameter id="ucldStdev.c:p4" lower="0.0" name="stateNode" upper="5.0">0.5</parameter>
- <stateNode dimension="58" id="rateCategories.c:p4" spec="parameter.IntegerParameter">1</stateNode>
<parameter id="ucldMean.c:p5" name="stateNode">1.0</parameter>
- <parameter id="ucldStdev.c:p5" lower="0.0" name="stateNode" upper="5.0">0.5</parameter>
- <stateNode dimension="58" id="rateCategories.c:p5" spec="parameter.IntegerParameter">1</stateNode>
</state>
<init birthRate="@birthRate.t:Species" estimate="false" id="SBI" popMean="@popMean" spec="beast.evolution.speciation.StarBeastStartState" speciesTree="@Tree.t:Species">
- <tree idref="Tree.t:p3" name="gene"/>
<tree idref="Tree.t:p1" name="gene"/>
- <tree idref="Tree.t:p2" name="gene"/>
<tree idref="Tree.t:p4" name="gene"/>
+ <tree idref="Tree.t:p2" name="gene"/>
+ <tree idref="Tree.t:p3" name="gene"/>
<tree idref="Tree.t:p5" name="gene"/>
<speciesTreePrior bottomPopSize="@popSize" gammaParameter="@popMean" id="SpeciesTreePopSize.Species" spec="beast.evolution.speciation.SpeciesTreePrior" taxonset="@taxonsuperset" tree="@Tree.t:Species"/>
</init>
@@ -210,11 +210,27 @@
4) same thing occurs if I start-over and only try cloning the RelaxedLogNormal clock to from p1 to p2-p5:
On standard error I get this printed to the screen:
Processin: TreeHeight.t:p1
Processin: treeTopFinder
Processin: UniformOperator.t:p1
Processin: ucldStdevScaler.c:p1
Processin: ucldStdevPrior.c:p1
Processin: SBI
Processin: CategoriesSwapOperator.c:p1
Processin: ucldMean.c:p1
Processin: narrow.t:p1
Processin: treeScaler.t:p1
Processin: wide.t:p1
Processin: TreeWithMetaDataLogger.t:p1
Processin: RealParameter.0
Processin: RelaxedClock.c:p1
Processin: CategoriesRandomWalk.c:p1
Processin: ucldMeanScaler.c:p1
Processin: CategoriesUniform.c:p1
Processin: TaxonSet.p1
Processin: rate.c:p1
Processin: relaxedUpDownOperator.c:p1
Processin: LogNormalDistributionModel.c:p1
Processin: updown.p1
Processin: MeanRatePrior.c:p1
Processin: WilsonBalding.t:p1
Processin: RandomGeneTree.t:p1
Processin: rateCategories.c:p1
Processin: treePrior.t:p1
Processin: SubtreeSlide.t:p1
Processin: ucldStdev.c:p1
Processin: SpeciesTreeLoggerX
Processin: Reheight.t:Species
Processin: updown.all.Species
Processin: strictClockUpDownOperator.c:p1
Processin: treeRootScaler.t:p1
Cannot find species with name Chlorella_vulgaris in species treeCannot find species with name Chlorella_vulgaris in species treeCannot find species with name Chlorella_vulgaris in species treeCannot find species with name Chlorella_vulgaris in species treeCannot find species with name Chlorella_vulgaris in species treeCannot find species with name Chlorella_vulgaris in species treeCannot find species with name Chlorella_vulgaris in species treeCannot find species with name Chlorella_vulgaris in species treeCannot find species with name Chlorella_vulgaris in species treeCannot find species with name Chlorella_vulgaris in species treeProcessin: Tree.t:p1
etc for each partition.
This is the "diff" of the XML where each partition was individuallyset to RelaxedLogNormal (runs without error) versus the XML from when it was cloned down (runs with error):
I would have expected these to be identical yet that is clearly not the case, although some of this is obviously just trivially different placements of elements. The stuff in <distribution id="speciescoalescent" seems to be the issue but I cant figure out how to fix it:
[cymon@spiro run4]$ diff -ruN relaxedLogNormal.xml cloned2.xml
--- relaxedLogNormal.xml 2014-11-12 16:26:16.236002409 +0000
+++ cloned2.xml 2014-11-12 16:37:35.320026425 +0000
@@ -84,12 +84,12 @@
<taxon id="Chaetosphaeridium_globosum" spec="TaxonSet">
<taxon id="Chaetosphaeridium_globosum_H" spec="Taxon"/>
</taxon>
- <taxon id="Selaginella_moellendorffii" spec="TaxonSet">
- <taxon id="Selaginella_moellendorffii_S" spec="Taxon"/>
- </taxon>
<taxon id="Nephroselmis_olivacea" spec="TaxonSet">
<taxon id="Nephroselmis_olivacea_D" spec="Taxon"/>
</taxon>
+ <taxon id="Selaginella_moellendorffii" spec="TaxonSet">
+ <taxon id="Selaginella_moellendorffii_S" spec="Taxon"/>
+ </taxon>
<taxon id="Mesostigma_viride" spec="TaxonSet">
<taxon id="Mesostigma_viride_E" spec="Taxon"/>
</taxon>
@@ -154,55 +154,55 @@
</tree>
<parameter id="birthRate.t:Species" lower="0.0" name="stateNode" upper="10000.0">213.2021</parameter>
<parameter id="popMean" name="stateNode">1.0</parameter>
- <tree id="Tree.t:p3" name="stateNode">
- <taxonset id="TaxonSet.p3" spec="TaxonSet">
- <alignment filter="6106-11544" id="p3" spec="FilteredAlignment">
+ <tree id="Tree.t:p1" name="stateNode">
+ <taxonset id="TaxonSet.p1" spec="TaxonSet">
+ <alignment filter="1-2907" id="p1" spec="FilteredAlignment">
<data
idref="roya2_concat_30taxon_nucl_incl_5partitions"/>
</alignment>
</taxonset>
</tree>
- <tree id="Tree.t:p1" name="stateNode">
- <taxonset id="TaxonSet.p1" spec="TaxonSet">
- <alignment data="@roya2_concat_30taxon_nucl_incl_5partitions" filter="1-2907" id="p1" spec="FilteredAlignment"/>
- </taxonset>
- </tree>
+ <parameter id="ucldStdev.c:p1" lower="0.0" name="stateNode" upper="5.0">0.5</parameter>
+ <stateNode dimension="58" id="rateCategories.c:p1" spec="parameter.IntegerParameter">1</stateNode>
<tree id="Tree.t:p2" name="stateNode">
<taxonset id="TaxonSet.p2" spec="TaxonSet">
<alignment data="@roya2_concat_30taxon_nucl_incl_5partitions" filter="2908-6105" id="p2" spec="FilteredAlignment"/>
</taxonset>
</tree>
+ <stateNode dimension="58" id="rateCategories.c:p2" spec="parameter.IntegerParameter">1</stateNode>
+ <parameter id="ucldStdev.c:p2" lower="0.0" name="stateNode" upper="5.0">0.5</parameter>
+ <tree id="Tree.t:p3" name="stateNode">
+ <taxonset id="TaxonSet.p3" spec="TaxonSet">
+ <alignment data="@roya2_concat_30taxon_nucl_incl_5partitions" filter="6106-11544" id="p3" spec="FilteredAlignment"/>
+ </taxonset>
+ </tree>
+ <stateNode dimension="58" id="rateCategories.c:p3" spec="parameter.IntegerParameter">1</stateNode>
+ <parameter id="ucldStdev.c:p3" lower="0.0" name="stateNode" upper="5.0">0.5</parameter>
<tree id="Tree.t:p4" name="stateNode">
<taxonset id="TaxonSet.p4" spec="TaxonSet">
<alignment data="@roya2_concat_30taxon_nucl_incl_5partitions" filter="11545-13599" id="p4" spec="FilteredAlignment"/>
</taxonset>
</tree>
+ <stateNode dimension="58" id="rateCategories.c:p4" spec="parameter.IntegerParameter">1</stateNode>
+ <parameter id="ucldStdev.c:p4" lower="0.0" name="stateNode" upper="5.0">0.5</parameter>
<tree id="Tree.t:p5" name="stateNode">
<taxonset id="TaxonSet.p5" spec="TaxonSet">
<alignment data="@roya2_concat_30taxon_nucl_incl_5partitions" filter="13600-20100" id="p5" spec="FilteredAlignment"/>
</taxonset>
</tree>
- <parameter id="ucldStdev.c:p1" lower="0.0" name="stateNode" upper="5.0">0.5</parameter>
- <stateNode dimension="58" id="rateCategories.c:p1" spec="parameter.IntegerParameter">1</stateNode>
+ <stateNode dimension="58" id="rateCategories.c:p5" spec="parameter.IntegerParameter">1</stateNode>
+ <parameter id="ucldStdev.c:p5" lower="0.0" name="stateNode" upper="5.0">0.5</parameter>
+ <parameter id="ucldMean.c:p4" name="stateNode">1.0</parameter>
<parameter id="ucldMean.c:p2" name="stateNode">1.0</parameter>
- <parameter id="ucldStdev.c:p2" lower="0.0" name="stateNode" upper="5.0">0.5</parameter>
- <stateNode dimension="58" id="rateCategories.c:p2" spec="parameter.IntegerParameter">1</stateNode>
<parameter id="ucldMean.c:p3" name="stateNode">1.0</parameter>
- <parameter id="ucldStdev.c:p3" lower="0.0" name="stateNode" upper="5.0">0.5</parameter>
- <stateNode dimension="58" id="rateCategories.c:p3" spec="parameter.IntegerParameter">1</stateNode>
- <parameter id="ucldMean.c:p4" name="stateNode">1.0</parameter>
- <parameter id="ucldStdev.c:p4" lower="0.0" name="stateNode" upper="5.0">0.5</parameter>
- <stateNode dimension="58" id="rateCategories.c:p4" spec="parameter.IntegerParameter">1</stateNode>
<parameter id="ucldMean.c:p5" name="stateNode">1.0</parameter>
- <parameter id="ucldStdev.c:p5" lower="0.0" name="stateNode" upper="5.0">0.5</parameter>
- <stateNode dimension="58" id="rateCategories.c:p5" spec="parameter.IntegerParameter">1</stateNode>
</state>
<init birthRate="@birthRate.t:Species" estimate="false" id="SBI" popMean="@popMean" spec="beast.evolution.speciation.StarBeastStartState" speciesTree="@Tree.t:Species">
- <tree idref="Tree.t:p3" name="gene"/>
<tree idref="Tree.t:p1" name="gene"/>
- <tree idref="Tree.t:p2" name="gene"/>
<tree idref="Tree.t:p4" name="gene"/>
+ <tree idref="Tree.t:p2" name="gene"/>
+ <tree idref="Tree.t:p3" name="gene"/>
<tree idref="Tree.t:p5" name="gene"/>
<speciesTreePrior bottomPopSize="@popSize" gammaParameter="@popMean" id="SpeciesTreePopSize.Species" spec="beast.evolution.speciation.SpeciesTreePrior" taxonset="@taxonsuperset" tree="@Tree.t:Species"/>
</init>
@@ -210,11 +210,27 @@
<distribution id="posterior" spec="util.CompoundDistribution">
<distribution id="speciescoalescent" spec="util.CompoundDistribution">
<distribution idref="SpeciesTreePopSize.Species"/>
- <distribution id="treePrior.t:p3" spec="beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution" speciesTree="@Tree.t:Species" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:p3"/>
<distribution id="treePrior.t:p1" spec="beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution" speciesTree="@Tree.t:Species" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:p1"/>
- <distribution id="treePrior.t:p2" spec="beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution" speciesTree="@Tree.t:Species" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:p2"/>
- <distribution id="treePrior.t:p4" spec="beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution" speciesTree="@Tree.t:Species" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:p4"/>
- <distribution id="treePrior.t:p5" spec="beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution" speciesTree="@Tree.t:Species" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:p5"/>
+ <distribution id="treePrior.t:p2" spec="beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:p2">
+ <tree id="Tree.t:p21" name="speciesTree">
+ <taxonset alignment="@p2" id="TaxonSet.p21" spec="TaxonSet"/>
+ </tree>
+ </distribution>
+ <distribution id="treePrior.t:p3" spec="beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:p3">
+ <tree id="Tree.t:p31" name="speciesTree">
+ <taxonset alignment="@p3" id="TaxonSet.p31" spec="TaxonSet"/>
+ </tree>
+ </distribution>
+ <distribution id="treePrior.t:p4" spec="beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:p4">
+ <tree id="Tree.t:p41" name="speciesTree">
+ <taxonset alignment="@p4" id="TaxonSet.p41" spec="TaxonSet"/>
+ </tree>
+ </distribution>
+ <distribution id="treePrior.t:p5" spec="beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:p5">
+ <tree id="Tree.t:p51" name="speciesTree">
+ <taxonset alignment="@p5" id="TaxonSet.p51" spec="TaxonSet"/>
+ </tree>
+ </distribution>
</distribution>
- <distribution id="treePrior.t:p3" spec="beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution" speciesTree="@Tree.t:Species" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:p3"/>
<distribution id="treePrior.t:p1" spec="beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution" speciesTree="@Tree.t:Species" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:p1"/>
- <distribution id="treePrior.t:p2" spec="beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution" speciesTree="@Tree.t:Species" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:p2"/>
- <distribution id="treePrior.t:p4" spec="beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution" speciesTree="@Tree.t:Species" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:p4"/>
- <distribution id="treePrior.t:p5" spec="beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution" speciesTree="@Tree.t:Species" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:p5"/>
+ <distribution id="treePrior.t:p2" spec="beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:p2">
+ <tree id="Tree.t:p21" name="speciesTree">
+ <taxonset alignment="@p2" id="TaxonSet.p21" spec="TaxonSet"/>
+ </tree>
+ </distribution>
+ <distribution id="treePrior.t:p3" spec="beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:p3">
+ <tree id="Tree.t:p31" name="speciesTree">
+ <taxonset alignment="@p3" id="TaxonSet.p31" spec="TaxonSet"/>
+ </tree>
+ </distribution>
+ <distribution id="treePrior.t:p4" spec="beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:p4">
+ <tree id="Tree.t:p41" name="speciesTree">
+ <taxonset alignment="@p4" id="TaxonSet.p41" spec="TaxonSet"/>
+ </tree>
+ </distribution>
+ <distribution id="treePrior.t:p5" spec="beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:p5">
+ <tree id="Tree.t:p51" name="speciesTree">
+ <taxonset alignment="@p5" id="TaxonSet.p51" spec="TaxonSet"/>
+ </tree>
+ </distribution>
</distribution>
<distribution id="prior" spec="util.CompoundDistribution">
<distribution birthDiffRate="@birthRate.t:Species" id="YuleModel.t:Species" spec="beast.evolution.speciation.YuleModel" tree="@Tree.t:Species"/>
@@ -229,38 +245,16 @@
<parameter estimate="false" id="RealParameter.0" name="mean">0.3333</parameter>
</Exponential>
</prior>
- <prior id="ucldStdevPrior.c:p2" name="distribution" x="@ucldStdev.c:p2">
- <Exponential id="Exponential.01" name="distr">
- <parameter estimate="false" id="RealParameter.01" name="mean">0.3333</parameter>
- </Exponential>
- </prior>
- <prior id="MeanRatePrior.c:p2" name="distribution" x="@ucldMean.c:p2">
- <Uniform id="Uniform.0" name="distr" upper="Infinity"/>
- </prior>
- <prior id="ucldStdevPrior.c:p3" name="distribution" x="@ucldStdev.c:p3">
- <Exponential id="Exponential.02" name="distr">
- <parameter estimate="false" id="RealParameter.02" name="mean">0.3333</parameter>
- </Exponential>
- </prior>
- <prior id="MeanRatePrior.c:p3" name="distribution" x="@ucldMean.c:p3">
- <Uniform id="Uniform.01" name="distr" upper="Infinity"/>
- </prior>
- <prior id="ucldStdevPrior.c:p4" name="distribution" x="@ucldStdev.c:p4">
- <Exponential id="Exponential.03" name="distr">
- <parameter estimate="false" id="RealParameter.03" name="mean">0.3333</parameter>
- </Exponential>
- </prior>
+ <prior distr="@Exponential.0" id="ucldStdevPrior.c:p2" name="distribution" x="@ucldStdev.c:p2"/>
+ <prior distr="@Exponential.0" id="ucldStdevPrior.c:p3" name="distribution" x="@ucldStdev.c:p3"/>
+ <prior distr="@Exponential.0" id="ucldStdevPrior.c:p4" name="distribution" x="@ucldStdev.c:p4"/>
+ <prior distr="@Exponential.0" id="ucldStdevPrior.c:p5" name="distribution" x="@ucldStdev.c:p5"/>
<prior id="MeanRatePrior.c:p4" name="distribution" x="@ucldMean.c:p4">
- <Uniform id="Uniform.02" name="distr" upper="Infinity"/>
- </prior>
- <prior id="ucldStdevPrior.c:p5" name="distribution" x="@ucldStdev.c:p5">
- <Exponential id="Exponential.04" name="distr">
- <parameter estimate="false" id="RealParameter.04" name="mean">0.3333</parameter>
- </Exponential>
- </prior>
- <prior id="MeanRatePrior.c:p5" name="distribution" x="@ucldMean.c:p5">
- <Uniform id="Uniform.03" name="distr" upper="Infinity"/>
+ <Uniform id="Uniform.0" name="distr" upper="Infinity"/>
</prior>
+ <prior distr="@Uniform.0" id="MeanRatePrior.c:p2" name="distribution" x="@ucldMean.c:p2"/>
+ <prior distr="@Uniform.0" id="MeanRatePrior.c:p3" name="distribution" x="@ucldMean.c:p3"/>
+ <prior distr="@Uniform.0" id="MeanRatePrior.c:p5" name="distribution" x="@ucldMean.c:p5"/>
</distribution>
<distribution id="likelihood" spec="util.CompoundDistribution">
<distribution data="@p1" id="treeLikelihood.p1" spec="TreeLikelihood" tree="@Tree.t:p1">
@@ -272,7 +266,7 @@
</siteModel>
<branchRateModel id="RelaxedClock.c:p1" rateCategories="@rateCategories.c:p1" spec="beast.evolution.branchratemodel.UCRelaxedClockModel" tree="@Tree.t:p1">
<LogNormal S="@ucldStdev.c:p1" id="LogNormalDistributionModel.c:p1" meanInRealSpace="true" name="distr">
- <parameter estimate="false" id="RealParameter.05" lower="0.0" name="M" upper="1.0">1.0</parameter>
+ <parameter estimate="false" id="RealParameter.01" lower="0.0" name="M" upper="1.0">1.0</parameter>
</LogNormal>
<parameter estimate="false" id="ucldMean.c:p1" name="clock.rate">1.0</parameter>
</branchRateModel>
@@ -286,7 +280,7 @@
</siteModel>
<branchRateModel clock.rate="@ucldMean.c:p2" id="RelaxedClock.c:p2" rateCategories="@rateCategories.c:p2" spec="beast.evolution.branchratemodel.UCRelaxedClockModel" tree="@Tree.t:p2">
<LogNormal S="@ucldStdev.c:p2" id="LogNormalDistributionModel.c:p2" meanInRealSpace="true" name="distr">
- <parameter estimate="false" id="RealParameter.06" lower="0.0" name="M" upper="1.0">1.0</parameter>
+ <parameter estimate="false" id="RealParameter.p2" lower="0.0" name="M" upper="1.0">1.0</parameter>
</LogNormal>
</branchRateModel>
</distribution>
@@ -299,7 +293,7 @@
</siteModel>
<branchRateModel clock.rate="@ucldMean.c:p3" id="RelaxedClock.c:p3" rateCategories="@rateCategories.c:p3" spec="beast.evolution.branchratemodel.UCRelaxedClockModel" tree="@Tree.t:p3">
<LogNormal S="@ucldStdev.c:p3" id="LogNormalDistributionModel.c:p3" meanInRealSpace="true" name="distr">
- <parameter estimate="false" id="RealParameter.07" lower="0.0" name="M" upper="1.0">1.0</parameter>
+ <parameter estimate="false" id="RealParameter.p3" lower="0.0" name="M" upper="1.0">1.0</parameter>
</LogNormal>
</branchRateModel>
</distribution>
@@ -312,7 +306,7 @@
</siteModel>
<branchRateModel clock.rate="@ucldMean.c:p4" id="RelaxedClock.c:p4" rateCategories="@rateCategories.c:p4" spec="beast.evolution.branchratemodel.UCRelaxedClockModel" tree="@Tree.t:p4">
<LogNormal S="@ucldStdev.c:p4" id="LogNormalDistributionModel.c:p4" meanInRealSpace="true" name="distr">
- <parameter estimate="false" id="RealParameter.08" lower="0.0" name="M" upper="1.0">1.0</parameter>
+ <parameter estimate="false" id="RealParameter.p4" lower="0.0" name="M" upper="1.0">1.0</parameter>
</LogNormal>
</branchRateModel>
</distribution>
@@ -325,52 +319,38 @@
</siteModel>
<branchRateModel clock.rate="@ucldMean.c:p5" id="RelaxedClock.c:p5" rateCategories="@rateCategories.c:p5" spec="beast.evolution.branchratemodel.UCRelaxedClockModel" tree="@Tree.t:p5">
<LogNormal S="@ucldStdev.c:p5" id="LogNormalDistributionModel.c:p5" meanInRealSpace="true" name="distr">
- <parameter estimate="false" id="RealParameter.09" lower="0.0" name="M" upper="1.0">1.0</parameter>
+ <parameter estimate="false" id="RealParameter.p5" lower="0.0" name="M" upper="1.0">1.0</parameter>
</LogNormal>
</branchRateModel>
</distribution>
</distribution>
</distribution>
- <operator id="Reheight.t:Species" spec="NodeReheight" taxonset="@taxonsuperset" tree="@Tree.t:Species" weight="101.708">
- <tree idref="Tree.t:p3" name="genetree"/>
+ <operator id="Reheight.t:Species" spec="NodeReheight" taxonset="@taxonsuperset" tree="@Tree.t:Species" weight="175.262624">
<tree idref="Tree.t:p1" name="genetree"/>
- <tree idref="Tree.t:p2" name="genetree"/>
<tree idref="Tree.t:p4" name="genetree"/>
+ <tree idref="Tree.t:p2" name="genetree"/>
+ <tree idref="Tree.t:p3" name="genetree"/>
<tree idref="Tree.t:p5" name="genetree"/>
</operator>
- <operator degreesOfFreedom="1" id="popSizeBottomScaler.t:Species" parameter="@popSize" scaleFactor="0.5" spec="ScaleOperator" weight="5.410000000000002"/>
+ <operator degreesOfFreedom="1" id="popSizeBottomScaler.t:Species" parameter="@popSize" scaleFactor="0.5" spec="ScaleOperator" weight="9.32248"/>
- <operator id="popMeanScale.t:Species" parameter="@popMean" scaleFactor="0.75" spec="ScaleOperator" weight="3.246000000000001"/>
+ <operator id="popMeanScale.t:Species" parameter="@popMean" scaleFactor="0.75" spec="ScaleOperator" weight="5.593488000000001"/>
- <operator id="updown.all.Species" scaleFactor="0.75" spec="UpDownOperator" weight="21.640000000000008">
+ <operator id="updown.all.Species" scaleFactor="0.75" spec="UpDownOperator" weight="37.28992">
<parameter idref="birthRate.t:Species" name="up"/>
<parameter idref="popMean" name="down"/>
<parameter idref="popSize" name="down"/>
<tree idref="Tree.t:Species" name="down"/>
- <tree idref="Tree.t:p3" name="down"/>
<tree idref="Tree.t:p1" name="down"/>
- <tree idref="Tree.t:p2" name="down"/>
<tree idref="Tree.t:p4" name="down"/>
+ <tree idref="Tree.t:p2" name="down"/>
+ <tree idref="Tree.t:p3" name="down"/>
<tree idref="Tree.t:p5" name="down"/>
</operator>
- <operator id="YuleBirthRateScaler.t:Species" parameter="@birthRate.t:Species" scaleFactor="0.75" spec="ScaleOperator" weight="3.246000000000001"/>
-
- <operator id="treeScaler.t:p3" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p3" weight="3.0"/>
-
- <operator id="treeRootScaler.t:p3" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p3" weight="3.0"/>
-
- <operator id="UniformOperator.t:p3" spec="Uniform" tree="@Tree.t:p3" weight="30.0"/>
-
- <operator id="SubtreeSlide.t:p3" spec="SubtreeSlide" tree="@Tree.t:p3" weight="15.0"/>
-
- <operator id="narrow.t:p3" spec="Exchange" tree="@Tree.t:p3" weight="15.0"/>
-
- <operator id="wide.t:p3" isNarrow="false" spec="Exchange" tree="@Tree.t:p3" weight="3.0"/>
-
- <operator id="WilsonBalding.t:p3" spec="WilsonBalding" tree="@Tree.t:p3" weight="3.0"/>
+ <operator id="YuleBirthRateScaler.t:Species" parameter="@birthRate.t:Species" scaleFactor="0.75" spec="ScaleOperator" weight="5.593488000000001"/>
<operator id="treeScaler.t:p1" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p1" weight="3.0"/>
@@ -386,110 +366,200 @@
<operator id="WilsonBalding.t:p1" spec="WilsonBalding" tree="@Tree.t:p1" weight="3.0"/>
- <operator id="treeScaler.t:p2" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p2" weight="3.0"/>
+ <operator id="ucldStdevScaler.c:p1" parameter="@ucldStdev.c:p1" scaleFactor="0.5" spec="ScaleOperator" weight="3.0"/>
- <operator id="treeRootScaler.t:p2" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p2" weight="3.0"/>
+ <operator id="CategoriesRandomWalk.c:p1" parameter="@rateCategories.c:p1" spec="IntRandomWalkOperator" weight="10.0" windowSize="1"/>
+
+ <operator id="CategoriesSwapOperator.c:p1" intparameter="@rateCategories.c:p1" spec="SwapOperator" weight="10.0"/>
+
+ <operator id="CategoriesUniform.c:p1" parameter="@rateCategories.c:p1" spec="UniformOperator" weight="10.0"/>
<operator id="UniformOperator.t:p2" spec="Uniform" tree="@Tree.t:p2" weight="30.0"/>
- <operator id="SubtreeSlide.t:p2" spec="SubtreeSlide" tree="@Tree.t:p2" weight="15.0"/>
+ <operator id="ucldStdevScaler.c:p2" parameter="@ucldStdev.c:p2" scaleFactor="0.5" spec="ScaleOperator" weight="3.0"/>
+
+ <operator id="CategoriesSwapOperator.c:p2" intparameter="@rateCategories.c:p2" spec="SwapOperator" weight="10.0"/>
<operator id="narrow.t:p2" spec="Exchange" tree="@Tree.t:p2" weight="15.0"/>
+ <operator id="treeScaler.t:p2" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p2" weight="3.0"/>
+
<operator id="wide.t:p2" isNarrow="false" spec="Exchange" tree="@Tree.t:p2" weight="3.0"/>
+ <operator id="CategoriesRandomWalk.c:p2" parameter="@rateCategories.c:p2" spec="IntRandomWalkOperator" weight="10.0" windowSize="1"/>
+
+ <operator id="CategoriesUniform.c:p2" parameter="@rateCategories.c:p2" spec="UniformOperator" weight="10.0"/>
+
<operator id="WilsonBalding.t:p2" spec="WilsonBalding" tree="@Tree.t:p2" weight="3.0"/>
- <operator id="treeScaler.t:p4" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p4" weight="3.0"/>
+ <operator id="SubtreeSlide.t:p2" spec="SubtreeSlide" tree="@Tree.t:p2" weight="15.0"/>
- <operator id="treeRootScaler.t:p4" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p4" weight="3.0"/>
+ <operator id="Reheight.t:p2" spec="NodeReheight" taxonset="@taxonsuperset" tree="@Tree.t:p2" weight="80.652">
+ <tree idref="Tree.t:p2" name="genetree"/>
+ <tree idref="Tree.t:p2" name="genetree"/>
+ <tree idref="Tree.t:p2" name="genetree"/>
+ <tree idref="Tree.t:p2" name="genetree"/>
+ </operator>
- <operator id="UniformOperator.t:p4" spec="Uniform" tree="@Tree.t:p4" weight="30.0"/>
+ <operator id="updown.p2" scaleFactor="0.75" spec="UpDownOperator" weight="17.16">
+ <parameter idref="birthRate.t:Species" name="up"/>
+ <parameter id="clockRate.c:p2" name="up">1.0</parameter>
+ <parameter idref="clockRate.c:p2" name="up"/>
+ <parameter idref="clockRate.c:p2" name="up"/>
+ <parameter idref="clockRate.c:p2" name="up"/>
+ <parameter idref="popMean" name="down"/>
+ <parameter idref="popSize" name="down"/>
+ <tree idref="Tree.t:p2" name="down"/>
+ <tree idref="Tree.t:p2" name="down"/>
+ <tree idref="Tree.t:p2" name="down"/>
+ <tree idref="Tree.t:p2" name="down"/>
+ <tree idref="Tree.t:p2" name="down"/>
+ </operator>
- <operator id="SubtreeSlide.t:p4" spec="SubtreeSlide" tree="@Tree.t:p4" weight="15.0"/>
+ <operator id="treeRootScaler.t:p2" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p2" weight="3.0"/>
- <operator id="narrow.t:p4" spec="Exchange" tree="@Tree.t:p4" weight="15.0"/>
+ <operator id="UniformOperator.t:p3" spec="Uniform" tree="@Tree.t:p3" weight="30.0"/>
- <operator id="wide.t:p4" isNarrow="false" spec="Exchange" tree="@Tree.t:p4" weight="3.0"/>
+ <operator id="ucldStdevScaler.c:p3" parameter="@ucldStdev.c:p3" scaleFactor="0.5" spec="ScaleOperator" weight="3.0"/>
- <operator id="WilsonBalding.t:p4" spec="WilsonBalding" tree="@Tree.t:p4" weight="3.0"/>
+ <operator id="CategoriesSwapOperator.c:p3" intparameter="@rateCategories.c:p3" spec="SwapOperator" weight="10.0"/>
- <operator id="treeScaler.t:p5" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p5" weight="3.0"/>
+ <operator id="narrow.t:p3" spec="Exchange" tree="@Tree.t:p3" weight="15.0"/>
- <operator id="treeRootScaler.t:p5" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p5" weight="3.0"/>
+ <operator id="treeScaler.t:p3" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p3" weight="3.0"/>
- <operator id="UniformOperator.t:p5" spec="Uniform" tree="@Tree.t:p5" weight="30.0"/>
+ <operator id="wide.t:p3" isNarrow="false" spec="Exchange" tree="@Tree.t:p3" weight="3.0"/>
- <operator id="SubtreeSlide.t:p5" spec="SubtreeSlide" tree="@Tree.t:p5" weight="15.0"/>
+ <operator id="CategoriesRandomWalk.c:p3" parameter="@rateCategories.c:p3" spec="IntRandomWalkOperator" weight="10.0" windowSize="1"/>
- <operator id="narrow.t:p5" spec="Exchange" tree="@Tree.t:p5" weight="15.0"/>
+ <operator id="CategoriesUniform.c:p3" parameter="@rateCategories.c:p3" spec="UniformOperator" weight="10.0"/>
- <operator id="wide.t:p5" isNarrow="false" spec="Exchange" tree="@Tree.t:p5" weight="3.0"/>
+ <operator id="WilsonBalding.t:p3" spec="WilsonBalding" tree="@Tree.t:p3" weight="3.0"/>
- <operator id="WilsonBalding.t:p5" spec="WilsonBalding" tree="@Tree.t:p5" weight="3.0"/>
+ <operator id="SubtreeSlide.t:p3" spec="SubtreeSlide" tree="@Tree.t:p3" weight="15.0"/>
- <operator id="ucldStdevScaler.c:p1" parameter="@ucldStdev.c:p1" scaleFactor="0.5" spec="ScaleOperator" weight="3.0"/>
+ <operator id="Reheight.t:p3" spec="NodeReheight" taxonset="@taxonsuperset" tree="@Tree.t:p3" weight="80.652">
+ <tree idref="Tree.t:p3" name="genetree"/>
+ <tree idref="Tree.t:p3" name="genetree"/>
+ <tree idref="Tree.t:p3" name="genetree"/>
+ </operator>
- <operator id="CategoriesRandomWalk.c:p1" parameter="@rateCategories.c:p1" spec="IntRandomWalkOperator" weight="10.0" windowSize="1"/>
+ <operator id="updown.p3" scaleFactor="0.75" spec="UpDownOperator" weight="17.16">
+ <parameter idref="birthRate.t:Species" name="up"/>
+ <parameter id="clockRate.c:p3" name="up">1.0</parameter>
+ <parameter idref="clockRate.c:p3" name="up"/>
+ <parameter idref="clockRate.c:p3" name="up"/>
+ <parameter idref="clockRate.c:p3" name="up"/>
+ <parameter idref="popMean" name="down"/>
+ <parameter idref="popSize" name="down"/>
+ <tree idref="Tree.t:p3" name="down"/>
+ <tree idref="Tree.t:p3" name="down"/>
+ <tree idref="Tree.t:p3" name="down"/>
+ <tree idref="Tree.t:p3" name="down"/>
+ </operator>
- <operator id="CategoriesSwapOperator.c:p1" intparameter="@rateCategories.c:p1" spec="SwapOperator" weight="10.0"/>
+ <operator id="treeRootScaler.t:p3" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p3" weight="3.0"/>
- <operator id="CategoriesUniform.c:p1" parameter="@rateCategories.c:p1" spec="UniformOperator" weight="10.0"/>
+ <operator id="UniformOperator.t:p4" spec="Uniform" tree="@Tree.t:p4" weight="30.0"/>
- <operator id="ucldMeanScaler.c:p2" parameter="@ucldMean.c:p2" scaleFactor="0.5" spec="ScaleOperator" weight="1.0"/>
+ <operator id="ucldStdevScaler.c:p4" parameter="@ucldStdev.c:p4" scaleFactor="0.5" spec="ScaleOperator" weight="3.0"/>
- <operator id="ucldStdevScaler.c:p2" parameter="@ucldStdev.c:p2" scaleFactor="0.5" spec="ScaleOperator" weight="3.0"/>
+ <operator id="CategoriesSwapOperator.c:p4" intparameter="@rateCategories.c:p4" spec="SwapOperator" weight="10.0"/>
- <operator id="CategoriesRandomWalk.c:p2" parameter="@rateCategories.c:p2" spec="IntRandomWalkOperator" weight="10.0" windowSize="1"/>
+ <operator id="narrow.t:p4" spec="Exchange" tree="@Tree.t:p4" weight="15.0"/>
- <operator id="CategoriesSwapOperator.c:p2" intparameter="@rateCategories.c:p2" spec="SwapOperator" weight="10.0"/>
+ <operator id="treeScaler.t:p4" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p4" weight="3.0"/>
- <operator id="CategoriesUniform.c:p2" parameter="@rateCategories.c:p2" spec="UniformOperator" weight="10.0"/>
+ <operator id="wide.t:p4" isNarrow="false" spec="Exchange" tree="@Tree.t:p4" weight="3.0"/>
- <operator id="relaxedUpDownOperator.c:p2" scaleFactor="0.75" spec="UpDownOperator" weight="3.0">
- <parameter idref="ucldMean.c:p2" name="up"/>
- <tree idref="Tree.t:p2" name="down"/>
+ <operator id="CategoriesRandomWalk.c:p4" parameter="@rateCategories.c:p4" spec="IntRandomWalkOperator" weight="10.0" windowSize="1"/>
+
+ <operator id="CategoriesUniform.c:p4" parameter="@rateCategories.c:p4" spec="UniformOperator" weight="10.0"/>
+
+ <operator id="WilsonBalding.t:p4" spec="WilsonBalding" tree="@Tree.t:p4" weight="3.0"/>
+
+ <operator id="SubtreeSlide.t:p4" spec="SubtreeSlide" tree="@Tree.t:p4" weight="15.0"/>
+
+ <operator id="Reheight.t:p4" spec="NodeReheight" taxonset="@taxonsuperset" tree="@Tree.t:p4" weight="80.652">
+ <tree idref="Tree.t:p4" name="genetree"/>
+ <tree idref="Tree.t:p4" name="genetree"/>
</operator>
- <operator id="ucldMeanScaler.c:p3" parameter="@ucldMean.c:p3" scaleFactor="0.5" spec="ScaleOperator" weight="1.0"/>
+ <operator id="updown.p4" scaleFactor="0.75" spec="UpDownOperator" weight="17.16">
+ <parameter idref="birthRate.t:Species" name="up"/>
+ <parameter id="clockRate.c:p4" name="up">1.0</parameter>
+ <parameter idref="clockRate.c:p4" name="up"/>
+ <parameter idref="clockRate.c:p4" name="up"/>
+ <parameter idref="clockRate.c:p4" name="up"/>
+ <parameter idref="popMean" name="down"/>
+ <parameter idref="popSize" name="down"/>
+ <tree idref="Tree.t:p4" name="down"/>
+ <tree idref="Tree.t:p4" name="down"/>
+ <tree idref="Tree.t:p4" name="down"/>
+ </operator>
- <operator id="ucldStdevScaler.c:p3" parameter="@ucldStdev.c:p3" scaleFactor="0.5" spec="ScaleOperator" weight="3.0"/>
+ <operator id="treeRootScaler.t:p4" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p4" weight="3.0"/>
- <operator id="CategoriesRandomWalk.c:p3" parameter="@rateCategories.c:p3" spec="IntRandomWalkOperator" weight="10.0" windowSize="1"/>
+ <operator id="UniformOperator.t:p5" spec="Uniform" tree="@Tree.t:p5" weight="30.0"/>
- <operator id="CategoriesSwapOperator.c:p3" intparameter="@rateCategories.c:p3" spec="SwapOperator" weight="10.0"/>
+ <operator id="ucldStdevScaler.c:p5" parameter="@ucldStdev.c:p5" scaleFactor="0.5" spec="ScaleOperator" weight="3.0"/>
- <operator id="CategoriesUniform.c:p3" parameter="@rateCategories.c:p3" spec="UniformOperator" weight="10.0"/>
+ <operator id="CategoriesSwapOperator.c:p5" intparameter="@rateCategories.c:p5" spec="SwapOperator" weight="10.0"/>
- <operator id="relaxedUpDownOperator.c:p3" scaleFactor="0.75" spec="UpDownOperator" weight="3.0">
- <parameter idref="ucldMean.c:p3" name="up"/>
- <tree idref="Tree.t:p3" name="down"/>
- </operator>
+ <operator id="narrow.t:p5" spec="Exchange" tree="@Tree.t:p5" weight="15.0"/>
- <operator id="ucldMeanScaler.c:p4" parameter="@ucldMean.c:p4" scaleFactor="0.5" spec="ScaleOperator" weight="1.0"/>
+ <operator id="treeScaler.t:p5" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p5" weight="3.0"/>
- <operator id="ucldStdevScaler.c:p4" parameter="@ucldStdev.c:p4" scaleFactor="0.5" spec="ScaleOperator" weight="3.0"/>
+ <operator id="wide.t:p5" isNarrow="false" spec="Exchange" tree="@Tree.t:p5" weight="3.0"/>
- <operator id="CategoriesRandomWalk.c:p4" parameter="@rateCategories.c:p4" spec="IntRandomWalkOperator" weight="10.0" windowSize="1"/>
+ <operator id="CategoriesRandomWalk.c:p5" parameter="@rateCategories.c:p5" spec="IntRandomWalkOperator" weight="10.0" windowSize="1"/>
- <operator id="CategoriesSwapOperator.c:p4" intparameter="@rateCategories.c:p4" spec="SwapOperator" weight="10.0"/>
+ <operator id="CategoriesUniform.c:p5" parameter="@rateCategories.c:p5" spec="UniformOperator" weight="10.0"/>
- <operator id="CategoriesUniform.c:p4" parameter="@rateCategories.c:p4" spec="UniformOperator" weight="10.0"/>
+ <operator id="WilsonBalding.t:p5" spec="WilsonBalding" tree="@Tree.t:p5" weight="3.0"/>
+
+ <operator id="SubtreeSlide.t:p5" spec="SubtreeSlide" tree="@Tree.t:p5" weight="15.0"/>
+
+ <operator id="Reheight.t:p5" spec="NodeReheight" taxonset="@taxonsuperset" tree="@Tree.t:p5" weight="80.652">
+ <tree idref="Tree.t:p5" name="genetree"/>
+ </operator>
+
+ <operator id="updown.p5" scaleFactor="0.75" spec="UpDownOperator" weight="17.16">
+ <parameter idref="birthRate.t:Species" name="up"/>
+ <parameter id="clockRate.c:p5" name="up">1.0</parameter>
+ <parameter idref="clockRate.c:p5" name="up"/>
+ <parameter idref="clockRate.c:p5" name="up"/>
+ <parameter idref="clockRate.c:p5" name="up"/>
+ <parameter idref="popMean" name="down"/>
+ <parameter idref="popSize" name="down"/>
+ <tree idref="Tree.t:p5" name="down"/>
+ <tree idref="Tree.t:p5" name="down"/>
+ </operator>
+
+ <operator id="treeRootScaler.t:p5" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p5" weight="3.0"/>
+
+ <operator id="ucldMeanScaler.c:p4" parameter="@ucldMean.c:p4" scaleFactor="0.5" spec="ScaleOperator" weight="1.0"/>
<operator id="relaxedUpDownOperator.c:p4" scaleFactor="0.75" spec="UpDownOperator" weight="3.0">
<parameter idref="ucldMean.c:p4" name="up"/>
<tree idref="Tree.t:p4" name="down"/>
</operator>
- <operator id="ucldMeanScaler.c:p5" parameter="@ucldMean.c:p5" scaleFactor="0.5" spec="ScaleOperator" weight="1.0"/>
+ <operator id="ucldMeanScaler.c:p2" parameter="@ucldMean.c:p2" scaleFactor="0.5" spec="ScaleOperator" weight="1.0"/>
- <operator id="ucldStdevScaler.c:p5" parameter="@ucldStdev.c:p5" scaleFactor="0.5" spec="ScaleOperator" weight="3.0"/>
+ <operator id="relaxedUpDownOperator.c:p2" scaleFactor="0.75" spec="UpDownOperator" weight="3.0">
+ <parameter idref="ucldMean.c:p2" name="up"/>
+ <tree idref="Tree.t:p2" name="down"/>
+ </operator>
- <operator id="CategoriesRandomWalk.c:p5" parameter="@rateCategories.c:p5" spec="IntRandomWalkOperator" weight="10.0" windowSize="1"/>
+ <operator id="ucldMeanScaler.c:p3" parameter="@ucldMean.c:p3" scaleFactor="0.5" spec="ScaleOperator" weight="1.0"/>
- <operator id="CategoriesSwapOperator.c:p5" intparameter="@rateCategories.c:p5" spec="SwapOperator" weight="10.0"/>
+ <operator id="relaxedUpDownOperator.c:p3" scaleFactor="0.75" spec="UpDownOperator" weight="3.0">
+ <parameter idref="ucldMean.c:p3" name="up"/>
+ <tree idref="Tree.t:p3" name="down"/>
+ </operator>
- <operator id="CategoriesUniform.c:p5" parameter="@rateCategories.c:p5" spec="UniformOperator" weight="10.0"/>
+ <operator id="ucldMeanScaler.c:p5" parameter="@ucldMean.c:p5" scaleFactor="0.5" spec="ScaleOperator" weight="1.0"/>
<operator id="relaxedUpDownOperator.c:p5" scaleFactor="0.75" spec="UpDownOperator" weight="3.0">
<parameter idref="ucldMean.c:p5" name="up"/>
@@ -504,44 +574,70 @@
<parameter idref="birthRate.t:Species" name="log"/>
<log idref="YuleModel.t:Species"/>
<log id="TreeHeight.Species" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:Species"/>
- <log idref="treeLikelihood.p3"/>
- <log idref="treePrior.t:p3"/>
- <log id="TreeHeight.t:p3" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:p3"/>
+ <log idref="treeLikelihood.p2"/>
<log idref="treeLikelihood.p1"/>
<log idref="treePrior.t:p1"/>
<log id="TreeHeight.t:p1" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:p1"/>
- <log idref="treeLikelihood.p2"/>
- <log idref="treePrior.t:p2"/>
- <log id="TreeHeight.t:p2" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:p2"/>
<log idref="treeLikelihood.p4"/>
- <log idref="treePrior.t:p4"/>
- <log id="TreeHeight.t:p4" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:p4"/>
+ <log idref="treeLikelihood.p3"/>
<log idref="treeLikelihood.p5"/>
- <log idref="treePrior.t:p5"/>
- <log id="TreeHeight.t:p5" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:p5"/>
<parameter idref="ucldStdev.c:p1" name="log"/>
<log branchratemodel="@RelaxedClock.c:p1" id="rate.c:p1" spec="beast.evolution.branchratemodel.RateStatistic" tree="@Tree.t:p1"/>
- <parameter idref="ucldMean.c:p2" name="log"/>
- <parameter idref="ucldStdev.c:p2" name="log"/>
+ <log id="TreeHeight.t:p2" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:p2"/>
<log branchratemodel="@RelaxedClock.c:p2" id="rate.c:p2" spec="beast.evolution.branchratemodel.RateStatistic" tree="@Tree.t:p2"/>
- <parameter idref="ucldMean.c:p3" name="log"/>
- <parameter idref="ucldStdev.c:p3" name="log"/>
+ <log idref="treePrior.t:p2"/>
+ <parameter idref="ucldStdev.c:p2" name="log"/>
+ <log id="TreeHeight.t:p3" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:p3"/>
<log branchratemodel="@RelaxedClock.c:p3" id="rate.c:p3" spec="beast.evolution.branchratemodel.RateStatistic" tree="@Tree.t:p3"/>
- <parameter idref="ucldMean.c:p4" name="log"/>
- <parameter idref="ucldStdev.c:p4" name="log"/>
+ <log idref="treePrior.t:p3"/>
+ <parameter idref="ucldStdev.c:p3" name="log"/>
+ <log id="TreeHeight.t:p4" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:p4"/>
<log branchratemodel="@RelaxedClock.c:p4" id="rate.c:p4" spec="beast.evolution.branchratemodel.RateStatistic" tree="@Tree.t:p4"/>
- <parameter idref="ucldMean.c:p5" name="log"/>
- <parameter idref="ucldStdev.c:p5" name="log"/>
+ <log idref="treePrior.t:p4"/>
+ <parameter idref="ucldStdev.c:p4" name="log"/>
+ <log id="TreeHeight.t:p5" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:p5"/>
<log branchratemodel="@RelaxedClock.c:p5" id="rate.c:p5" spec="beast.evolution.branchratemodel.RateStatistic" tree="@Tree.t:p5"/>
+ <log idref="treePrior.t:p5"/>
+ <parameter idref="ucldStdev.c:p5" name="log"/>
+ <parameter idref="ucldMean.c:p4" name="log"/>
+ <parameter idref="ucldMean.c:p2" name="log"/>
+ <parameter idref="ucldMean.c:p3" name="log"/>
+ <parameter idref="ucldMean.c:p5" name="log"/>
</logger>
<logger fileName="species_$(seed).trees" id="speciesTreeLogger" logEvery="5000" mode="tree">
<log id="SpeciesTreeLoggerX" popSize="@popSize" spec="beast.evolution.speciation.SpeciesTreeLogger" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:Species">
<treetop id="treeTopFinder" spec="beast.evolution.speciation.TreeTopFinder">
- <tree idref="Tree.t:p3"/>
<tree idref="Tree.t:p1"/>
+ <tree idref="Tree.t:p4"/>
+ <tree idref="Tree.t:p2"/>
+ <tree idref="Tree.t:p3"/>
+ <tree idref="Tree.t:p5"/>
+ </treetop>
+ </log>
+ <log id="p21" popSize="@popSize" spec="beast.evolution.speciation.SpeciesTreeLogger" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:p2">
+ <treetop id="p22" spec="beast.evolution.speciation.TreeTopFinder">
+ <tree idref="Tree.t:p2"/>
<tree idref="Tree.t:p2"/>
+ <tree idref="Tree.t:p2"/>
+ <tree idref="Tree.t:p2"/>
+ </treetop>
+ </log>
+ <log id="p31" popSize="@popSize" spec="beast.evolution.speciation.SpeciesTreeLogger" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:p3">
+ <treetop id="p32" spec="beast.evolution.speciation.TreeTopFinder">
+ <tree idref="Tree.t:p3"/>
+ <tree idref="Tree.t:p3"/>
+ <tree idref="Tree.t:p3"/>
+ </treetop>
+ </log>
+ <log id="p41" popSize="@popSize" spec="beast.evolution.speciation.SpeciesTreeLogger" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:p4">
+ <treetop id="p42" spec="beast.evolution.speciation.TreeTopFinder">
+ <tree idref="Tree.t:p4"/>
<tree idref="Tree.t:p4"/>
+ </treetop>
+ </log>
+ <log id="p51" popSize="@popSize" spec="beast.evolution.speciation.SpeciesTreeLogger" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:p5">
+ <treetop id="p52" spec="beast.evolution.speciation.TreeTopFinder">
<tree idref="Tree.t:p5"/>
</treetop>
</log>
@@ -554,22 +650,22 @@
<log idref="prior"/>
</logger>
- <logger fileName="$(tree).$(seed).trees" id="treelog.t:p3" logEvery="5000" mode="tree">
- <log branchratemodel="@RelaxedClock.c:p3" id="TreeWithMetaDataLogger.t:p3" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:p3"/>
+ <logger fileName="$(tree).$(seed).trees" id="treelog.t:p2" logEvery="5000" mode="tree">
+ <log branchratemodel="@RelaxedClock.c:p2" id="TreeWithMetaDataLogger.t:p2" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:p2"/>
</logger>
<logger fileName="$(tree).$(seed).trees" id="treelog.t:p1" logEvery="5000" mode="tree">
<log branchratemodel="@RelaxedClock.c:p1" id="TreeWithMetaDataLogger.t:p1" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:p1"/>
</logger>
- <logger fileName="$(tree).$(seed).trees" id="treelog.t:p2" logEvery="5000" mode="tree">
- <log branchratemodel="@RelaxedClock.c:p2" id="TreeWithMetaDataLogger.t:p2" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:p2"/>
- </logger>
-
<logger fileName="$(tree).$(seed).trees" id="treelog.t:p4" logEvery="5000" mode="tree">
<log branchratemodel="@RelaxedClock.c:p4" id="TreeWithMetaDataLogger.t:p4" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:p4"/>
</logger>
+ <logger fileName="$(tree).$(seed).trees" id="treelog.t:p3" logEvery="5000" mode="tree">
+ <log branchratemodel="@RelaxedClock.c:p3" id="TreeWithMetaDataLogger.t:p3" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:p3"/>
+ </logger>
+
<logger fileName="$(tree).$(seed).trees" id="treelog.t:p5" logEvery="5000" mode="tree">
<log branchratemodel="@RelaxedClock.c:p5" id="TreeWithMetaDataLogger.t:p5" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:p5"/>
</logger>
Regards, Cymon
@@ -229,38 +245,16 @@
<parameter estimate="false" id="RealParameter.0" name="mean">0.3333</parameter>
</Exponential>
</prior>
- <prior id="ucldStdevPrior.c:p2" name="distribution" x="@ucldStdev.c:p2">
- <Exponential id="Exponential.01" name="distr">
- <parameter estimate="false" id="RealParameter.01" name="mean">0.3333</parameter>
- </Exponential>
- </prior>
- <prior id="MeanRatePrior.c:p2" name="distribution" x="@ucldMean.c:p2">
- <Uniform id="Uniform.0" name="distr" upper="Infinity"/>
- </prior>
- <prior id="ucldStdevPrior.c:p3" name="distribution" x="@ucldStdev.c:p3">
- <Exponential id="Exponential.02" name="distr">
- <parameter estimate="false" id="RealParameter.02" name="mean">0.3333</parameter>
- </Exponential>
- </prior>
- <prior id="MeanRatePrior.c:p3" name="distribution" x="@ucldMean.c:p3">
- <Uniform id="Uniform.01" name="distr" upper="Infinity"/>
- </prior>
- <prior id="ucldStdevPrior.c:p4" name="distribution" x="@ucldStdev.c:p4">
- <Exponential id="Exponential.03" name="distr">
- <parameter estimate="false" id="RealParameter.03" name="mean">0.3333</parameter>
- </Exponential>
- </prior>
+ <prior distr="@Exponential.0" id="ucldStdevPrior.c:p2" name="distribution" x="@ucldStdev.c:p2"/>
+ <prior distr="@Exponential.0" id="ucldStdevPrior.c:p3" name="distribution" x="@ucldStdev.c:p3"/>
+ <prior distr="@Exponential.0" id="ucldStdevPrior.c:p4" name="distribution" x="@ucldStdev.c:p4"/>
+ <prior distr="@Exponential.0" id="ucldStdevPrior.c:p5" name="distribution" x="@ucldStdev.c:p5"/>
<prior id="MeanRatePrior.c:p4" name="distribution" x="@ucldMean.c:p4">
- <Uniform id="Uniform.02" name="distr" upper="Infinity"/>
- </prior>
- <prior id="ucldStdevPrior.c:p5" name="distribution" x="@ucldStdev.c:p5">
- <Exponential id="Exponential.04" name="distr">
- <parameter estimate="false" id="RealParameter.04" name="mean">0.3333</parameter>
- </Exponential>
- </prior>
- <prior id="MeanRatePrior.c:p5" name="distribution" x="@ucldMean.c:p5">
- <Uniform id="Uniform.03" name="distr" upper="Infinity"/>
+ <Uniform id="Uniform.0" name="distr" upper="Infinity"/>
</prior>
+ <prior distr="@Uniform.0" id="MeanRatePrior.c:p2" name="distribution" x="@ucldMean.c:p2"/>
+ <prior distr="@Uniform.0" id="MeanRatePrior.c:p3" name="distribution" x="@ucldMean.c:p3"/>
+ <prior distr="@Uniform.0" id="MeanRatePrior.c:p5" name="distribution" x="@ucldMean.c:p5"/>
</distribution>
<distribution id="likelihood" spec="util.CompoundDistribution">
<distribution data="@p1" id="treeLikelihood.p1" spec="TreeLikelihood" tree="@Tree.t:p1">
@@ -272,7 +266,7 @@
</siteModel>
<branchRateModel id="RelaxedClock.c:p1" rateCategories="@rateCategories.c:p1" spec="beast.evolution.branchratemodel.UCRelaxedClockModel" tree="@Tree.t:p1">
<LogNormal S="@ucldStdev.c:p1" id="LogNormalDistributionModel.c:p1" meanInRealSpace="true" name="distr">
- <parameter estimate="false" id="RealParameter.05" lower="0.0" name="M" upper="1.0">1.0</parameter>
+ <parameter estimate="false" id="RealParameter.01" lower="0.0" name="M" upper="1.0">1.0</parameter>
</LogNormal>
<parameter estimate="false" id="ucldMean.c:p1" name="clock.rate">1.0</parameter>
</branchRateModel>
@@ -286,7 +280,7 @@
</siteModel>
<branchRateModel clock.rate="@ucldMean.c:p2" id="RelaxedClock.c:p2" rateCategories="@rateCategories.c:p2" spec="beast.evolution.branchratemodel.UCRelaxedClockModel" tree="@Tree.t:p2">
<LogNormal S="@ucldStdev.c:p2" id="LogNormalDistributionModel.c:p2" meanInRealSpace="true" name="distr">
- <parameter estimate="false" id="RealParameter.06" lower="0.0" name="M" upper="1.0">1.0</parameter>
+ <parameter estimate="false" id="RealParameter.p2" lower="0.0" name="M" upper="1.0">1.0</parameter>
</LogNormal>
</branchRateModel>
</distribution>
@@ -299,7 +293,7 @@
</siteModel>
<branchRateModel clock.rate="@ucldMean.c:p3" id="RelaxedClock.c:p3" rateCategories="@rateCategories.c:p3" spec="beast.evolution.branchratemodel.UCRelaxedClockModel" tree="@Tree.t:p3">
<LogNormal S="@ucldStdev.c:p3" id="LogNormalDistributionModel.c:p3" meanInRealSpace="true" name="distr">
- <parameter estimate="false" id="RealParameter.07" lower="0.0" name="M" upper="1.0">1.0</parameter>
+ <parameter estimate="false" id="RealParameter.p3" lower="0.0" name="M" upper="1.0">1.0</parameter>
</LogNormal>
</branchRateModel>
</distribution>
@@ -312,7 +306,7 @@
</siteModel>
<branchRateModel clock.rate="@ucldMean.c:p4" id="RelaxedClock.c:p4" rateCategories="@rateCategories.c:p4" spec="beast.evolution.branchratemodel.UCRelaxedClockModel" tree="@Tree.t:p4">
<LogNormal S="@ucldStdev.c:p4" id="LogNormalDistributionModel.c:p4" meanInRealSpace="true" name="distr">
- <parameter estimate="false" id="RealParameter.08" lower="0.0" name="M" upper="1.0">1.0</parameter>
+ <parameter estimate="false" id="RealParameter.p4" lower="0.0" name="M" upper="1.0">1.0</parameter>
</LogNormal>
</branchRateModel>
</distribution>
@@ -325,52 +319,38 @@
</siteModel>
<branchRateModel clock.rate="@ucldMean.c:p5" id="RelaxedClock.c:p5" rateCategories="@rateCategories.c:p5" spec="beast.evolution.branchratemodel.UCRelaxedClockModel" tree="@Tree.t:p5">
<LogNormal S="@ucldStdev.c:p5" id="LogNormalDistributionModel.c:p5" meanInRealSpace="true" name="distr">
- <parameter estimate="false" id="RealParameter.09" lower="0.0" name="M" upper="1.0">1.0</parameter>
+ <parameter estimate="false" id="RealParameter.p5" lower="0.0" name="M" upper="1.0">1.0</parameter>
</LogNormal>
</branchRateModel>
</distribution>
</distribution>
</distribution>
- <operator id="Reheight.t:Species" spec="NodeReheight" taxonset="@taxonsuperset" tree="@Tree.t:Species" weight="101.708">
- <tree idref="Tree.t:p3" name="genetree"/>
+ <operator id="Reheight.t:Species" spec="NodeReheight" taxonset="@taxonsuperset" tree="@Tree.t:Species" weight="175.262624">
<tree idref="Tree.t:p1" name="genetree"/>
- <tree idref="Tree.t:p2" name="genetree"/>
<tree idref="Tree.t:p4" name="genetree"/>
+ <tree idref="Tree.t:p2" name="genetree"/>
+ <tree idref="Tree.t:p3" name="genetree"/>
<tree idref="Tree.t:p5" name="genetree"/>
</operator>
- <operator degreesOfFreedom="1" id="popSizeBottomScaler.t:Species" parameter="@popSize" scaleFactor="0.5" spec="ScaleOperator" weight="5.410000000000002"/>
+ <operator degreesOfFreedom="1" id="popSizeBottomScaler.t:Species" parameter="@popSize" scaleFactor="0.5" spec="ScaleOperator" weight="9.32248"/>
- <operator id="popMeanScale.t:Species" parameter="@popMean" scaleFactor="0.75" spec="ScaleOperator" weight="3.246000000000001"/>
+ <operator id="popMeanScale.t:Species" parameter="@popMean" scaleFactor="0.75" spec="ScaleOperator" weight="5.593488000000001"/>
- <operator id="updown.all.Species" scaleFactor="0.75" spec="UpDownOperator" weight="21.640000000000008">
+ <operator id="updown.all.Species" scaleFactor="0.75" spec="UpDownOperator" weight="37.28992">
<parameter idref="birthRate.t:Species" name="up"/>
<parameter idref="popMean" name="down"/>
<parameter idref="popSize" name="down"/>
<tree idref="Tree.t:Species" name="down"/>
- <tree idref="Tree.t:p3" name="down"/>
<tree idref="Tree.t:p1" name="down"/>
- <tree idref="Tree.t:p2" name="down"/>
<tree idref="Tree.t:p4" name="down"/>
+ <tree idref="Tree.t:p2" name="down"/>
+ <tree idref="Tree.t:p3" name="down"/>
<tree idref="Tree.t:p5" name="down"/>
</operator>
- <operator id="YuleBirthRateScaler.t:Species" parameter="@birthRate.t:Species" scaleFactor="0.75" spec="ScaleOperator" weight="3.246000000000001"/>
-
- <operator id="treeScaler.t:p3" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p3" weight="3.0"/>
-
- <operator id="treeRootScaler.t:p3" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p3" weight="3.0"/>
-
- <operator id="UniformOperator.t:p3" spec="Uniform" tree="@Tree.t:p3" weight="30.0"/>
-
- <operator id="SubtreeSlide.t:p3" spec="SubtreeSlide" tree="@Tree.t:p3" weight="15.0"/>
-
- <operator id="narrow.t:p3" spec="Exchange" tree="@Tree.t:p3" weight="15.0"/>
-
- <operator id="wide.t:p3" isNarrow="false" spec="Exchange" tree="@Tree.t:p3" weight="3.0"/>
-
- <operator id="WilsonBalding.t:p3" spec="WilsonBalding" tree="@Tree.t:p3" weight="3.0"/>
+ <operator id="YuleBirthRateScaler.t:Species" parameter="@birthRate.t:Species" scaleFactor="0.75" spec="ScaleOperator" weight="5.593488000000001"/>
<operator id="treeScaler.t:p1" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p1" weight="3.0"/>
@@ -386,110 +366,200 @@
<operator id="WilsonBalding.t:p1" spec="WilsonBalding" tree="@Tree.t:p1" weight="3.0"/>
- <operator id="treeScaler.t:p2" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p2" weight="3.0"/>
+ <operator id="ucldStdevScaler.c:p1" parameter="@ucldStdev.c:p1" scaleFactor="0.5" spec="ScaleOperator" weight="3.0"/>
- <operator id="treeRootScaler.t:p2" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p2" weight="3.0"/>
+ <operator id="CategoriesRandomWalk.c:p1" parameter="@rateCategories.c:p1" spec="IntRandomWalkOperator" weight="10.0" windowSize="1"/>
+
+ <operator id="CategoriesSwapOperator.c:p1" intparameter="@rateCategories.c:p1" spec="SwapOperator" weight="10.0"/>
+
+ <operator id="CategoriesUniform.c:p1" parameter="@rateCategories.c:p1" spec="UniformOperator" weight="10.0"/>
<operator id="UniformOperator.t:p2" spec="Uniform" tree="@Tree.t:p2" weight="30.0"/>
- <operator id="SubtreeSlide.t:p2" spec="SubtreeSlide" tree="@Tree.t:p2" weight="15.0"/>
+ <operator id="ucldStdevScaler.c:p2" parameter="@ucldStdev.c:p2" scaleFactor="0.5" spec="ScaleOperator" weight="3.0"/>
+
+ <operator id="CategoriesSwapOperator.c:p2" intparameter="@rateCategories.c:p2" spec="SwapOperator" weight="10.0"/>
<operator id="narrow.t:p2" spec="Exchange" tree="@Tree.t:p2" weight="15.0"/>
+ <operator id="treeScaler.t:p2" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p2" weight="3.0"/>
+
<operator id="wide.t:p2" isNarrow="false" spec="Exchange" tree="@Tree.t:p2" weight="3.0"/>
+ <operator id="CategoriesRandomWalk.c:p2" parameter="@rateCategories.c:p2" spec="IntRandomWalkOperator" weight="10.0" windowSize="1"/>
+
+ <operator id="CategoriesUniform.c:p2" parameter="@rateCategories.c:p2" spec="UniformOperator" weight="10.0"/>
+
<operator id="WilsonBalding.t:p2" spec="WilsonBalding" tree="@Tree.t:p2" weight="3.0"/>
- <operator id="treeScaler.t:p4" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p4" weight="3.0"/>
+ <operator id="SubtreeSlide.t:p2" spec="SubtreeSlide" tree="@Tree.t:p2" weight="15.0"/>
- <operator id="treeRootScaler.t:p4" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p4" weight="3.0"/>
+ <operator id="Reheight.t:p2" spec="NodeReheight" taxonset="@taxonsuperset" tree="@Tree.t:p2" weight="80.652">
+ <tree idref="Tree.t:p2" name="genetree"/>
+ <tree idref="Tree.t:p2" name="genetree"/>
+ <tree idref="Tree.t:p2" name="genetree"/>
+ <tree idref="Tree.t:p2" name="genetree"/>
+ </operator>
- <operator id="UniformOperator.t:p4" spec="Uniform" tree="@Tree.t:p4" weight="30.0"/>
+ <operator id="updown.p2" scaleFactor="0.75" spec="UpDownOperator" weight="17.16">
+ <parameter idref="birthRate.t:Species" name="up"/>
+ <parameter id="clockRate.c:p2" name="up">1.0</parameter>
+ <parameter idref="clockRate.c:p2" name="up"/>
+ <parameter idref="clockRate.c:p2" name="up"/>
+ <parameter idref="clockRate.c:p2" name="up"/>
+ <parameter idref="popMean" name="down"/>
+ <parameter idref="popSize" name="down"/>
+ <tree idref="Tree.t:p2" name="down"/>
+ <tree idref="Tree.t:p2" name="down"/>
+ <tree idref="Tree.t:p2" name="down"/>
+ <tree idref="Tree.t:p2" name="down"/>
+ <tree idref="Tree.t:p2" name="down"/>
+ </operator>
- <operator id="SubtreeSlide.t:p4" spec="SubtreeSlide" tree="@Tree.t:p4" weight="15.0"/>
+ <operator id="treeRootScaler.t:p2" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p2" weight="3.0"/>
- <operator id="narrow.t:p4" spec="Exchange" tree="@Tree.t:p4" weight="15.0"/>
+ <operator id="UniformOperator.t:p3" spec="Uniform" tree="@Tree.t:p3" weight="30.0"/>
- <operator id="wide.t:p4" isNarrow="false" spec="Exchange" tree="@Tree.t:p4" weight="3.0"/>
+ <operator id="ucldStdevScaler.c:p3" parameter="@ucldStdev.c:p3" scaleFactor="0.5" spec="ScaleOperator" weight="3.0"/>
- <operator id="WilsonBalding.t:p4" spec="WilsonBalding" tree="@Tree.t:p4" weight="3.0"/>
+ <operator id="CategoriesSwapOperator.c:p3" intparameter="@rateCategories.c:p3" spec="SwapOperator" weight="10.0"/>
- <operator id="treeScaler.t:p5" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p5" weight="3.0"/>
+ <operator id="narrow.t:p3" spec="Exchange" tree="@Tree.t:p3" weight="15.0"/>
- <operator id="treeRootScaler.t:p5" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p5" weight="3.0"/>
+ <operator id="treeScaler.t:p3" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p3" weight="3.0"/>
- <operator id="UniformOperator.t:p5" spec="Uniform" tree="@Tree.t:p5" weight="30.0"/>
+ <operator id="wide.t:p3" isNarrow="false" spec="Exchange" tree="@Tree.t:p3" weight="3.0"/>
- <operator id="SubtreeSlide.t:p5" spec="SubtreeSlide" tree="@Tree.t:p5" weight="15.0"/>
+ <operator id="CategoriesRandomWalk.c:p3" parameter="@rateCategories.c:p3" spec="IntRandomWalkOperator" weight="10.0" windowSize="1"/>
- <operator id="narrow.t:p5" spec="Exchange" tree="@Tree.t:p5" weight="15.0"/>
+ <operator id="CategoriesUniform.c:p3" parameter="@rateCategories.c:p3" spec="UniformOperator" weight="10.0"/>
- <operator id="wide.t:p5" isNarrow="false" spec="Exchange" tree="@Tree.t:p5" weight="3.0"/>
+ <operator id="WilsonBalding.t:p3" spec="WilsonBalding" tree="@Tree.t:p3" weight="3.0"/>
- <operator id="WilsonBalding.t:p5" spec="WilsonBalding" tree="@Tree.t:p5" weight="3.0"/>
+ <operator id="SubtreeSlide.t:p3" spec="SubtreeSlide" tree="@Tree.t:p3" weight="15.0"/>
- <operator id="ucldStdevScaler.c:p1" parameter="@ucldStdev.c:p1" scaleFactor="0.5" spec="ScaleOperator" weight="3.0"/>
+ <operator id="Reheight.t:p3" spec="NodeReheight" taxonset="@taxonsuperset" tree="@Tree.t:p3" weight="80.652">
+ <tree idref="Tree.t:p3" name="genetree"/>
+ <tree idref="Tree.t:p3" name="genetree"/>
+ <tree idref="Tree.t:p3" name="genetree"/>
+ </operator>
- <operator id="CategoriesRandomWalk.c:p1" parameter="@rateCategories.c:p1" spec="IntRandomWalkOperator" weight="10.0" windowSize="1"/>
+ <operator id="updown.p3" scaleFactor="0.75" spec="UpDownOperator" weight="17.16">
+ <parameter idref="birthRate.t:Species" name="up"/>
+ <parameter id="clockRate.c:p3" name="up">1.0</parameter>
+ <parameter idref="clockRate.c:p3" name="up"/>
+ <parameter idref="clockRate.c:p3" name="up"/>
+ <parameter idref="clockRate.c:p3" name="up"/>
+ <parameter idref="popMean" name="down"/>
+ <parameter idref="popSize" name="down"/>
+ <tree idref="Tree.t:p3" name="down"/>
+ <tree idref="Tree.t:p3" name="down"/>
+ <tree idref="Tree.t:p3" name="down"/>
+ <tree idref="Tree.t:p3" name="down"/>
+ </operator>
- <operator id="CategoriesSwapOperator.c:p1" intparameter="@rateCategories.c:p1" spec="SwapOperator" weight="10.0"/>
+ <operator id="treeRootScaler.t:p3" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p3" weight="3.0"/>
- <operator id="CategoriesUniform.c:p1" parameter="@rateCategories.c:p1" spec="UniformOperator" weight="10.0"/>
+ <operator id="UniformOperator.t:p4" spec="Uniform" tree="@Tree.t:p4" weight="30.0"/>
- <operator id="ucldMeanScaler.c:p2" parameter="@ucldMean.c:p2" scaleFactor="0.5" spec="ScaleOperator" weight="1.0"/>
+ <operator id="ucldStdevScaler.c:p4" parameter="@ucldStdev.c:p4" scaleFactor="0.5" spec="ScaleOperator" weight="3.0"/>
- <operator id="ucldStdevScaler.c:p2" parameter="@ucldStdev.c:p2" scaleFactor="0.5" spec="ScaleOperator" weight="3.0"/>
+ <operator id="CategoriesSwapOperator.c:p4" intparameter="@rateCategories.c:p4" spec="SwapOperator" weight="10.0"/>
- <operator id="CategoriesRandomWalk.c:p2" parameter="@rateCategories.c:p2" spec="IntRandomWalkOperator" weight="10.0" windowSize="1"/>
+ <operator id="narrow.t:p4" spec="Exchange" tree="@Tree.t:p4" weight="15.0"/>
- <operator id="CategoriesSwapOperator.c:p2" intparameter="@rateCategories.c:p2" spec="SwapOperator" weight="10.0"/>
+ <operator id="treeScaler.t:p4" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p4" weight="3.0"/>
- <operator id="CategoriesUniform.c:p2" parameter="@rateCategories.c:p2" spec="UniformOperator" weight="10.0"/>
+ <operator id="wide.t:p4" isNarrow="false" spec="Exchange" tree="@Tree.t:p4" weight="3.0"/>
- <operator id="relaxedUpDownOperator.c:p2" scaleFactor="0.75" spec="UpDownOperator" weight="3.0">
- <parameter idref="ucldMean.c:p2" name="up"/>
- <tree idref="Tree.t:p2" name="down"/>
+ <operator id="CategoriesRandomWalk.c:p4" parameter="@rateCategories.c:p4" spec="IntRandomWalkOperator" weight="10.0" windowSize="1"/>
+
+ <operator id="CategoriesUniform.c:p4" parameter="@rateCategories.c:p4" spec="UniformOperator" weight="10.0"/>
+
+ <operator id="WilsonBalding.t:p4" spec="WilsonBalding" tree="@Tree.t:p4" weight="3.0"/>
+
+ <operator id="SubtreeSlide.t:p4" spec="SubtreeSlide" tree="@Tree.t:p4" weight="15.0"/>
+
+ <operator id="Reheight.t:p4" spec="NodeReheight" taxonset="@taxonsuperset" tree="@Tree.t:p4" weight="80.652">
+ <tree idref="Tree.t:p4" name="genetree"/>
+ <tree idref="Tree.t:p4" name="genetree"/>
</operator>
- <operator id="ucldMeanScaler.c:p3" parameter="@ucldMean.c:p3" scaleFactor="0.5" spec="ScaleOperator" weight="1.0"/>
+ <operator id="updown.p4" scaleFactor="0.75" spec="UpDownOperator" weight="17.16">
+ <parameter idref="birthRate.t:Species" name="up"/>
+ <parameter id="clockRate.c:p4" name="up">1.0</parameter>
+ <parameter idref="clockRate.c:p4" name="up"/>
+ <parameter idref="clockRate.c:p4" name="up"/>
+ <parameter idref="clockRate.c:p4" name="up"/>
+ <parameter idref="popMean" name="down"/>
+ <parameter idref="popSize" name="down"/>
+ <tree idref="Tree.t:p4" name="down"/>
+ <tree idref="Tree.t:p4" name="down"/>
+ <tree idref="Tree.t:p4" name="down"/>
+ </operator>
- <operator id="ucldStdevScaler.c:p3" parameter="@ucldStdev.c:p3" scaleFactor="0.5" spec="ScaleOperator" weight="3.0"/>
+ <operator id="treeRootScaler.t:p4" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p4" weight="3.0"/>
- <operator id="CategoriesRandomWalk.c:p3" parameter="@rateCategories.c:p3" spec="IntRandomWalkOperator" weight="10.0" windowSize="1"/>
+ <operator id="UniformOperator.t:p5" spec="Uniform" tree="@Tree.t:p5" weight="30.0"/>
- <operator id="CategoriesSwapOperator.c:p3" intparameter="@rateCategories.c:p3" spec="SwapOperator" weight="10.0"/>
+ <operator id="ucldStdevScaler.c:p5" parameter="@ucldStdev.c:p5" scaleFactor="0.5" spec="ScaleOperator" weight="3.0"/>
- <operator id="CategoriesUniform.c:p3" parameter="@rateCategories.c:p3" spec="UniformOperator" weight="10.0"/>
+ <operator id="CategoriesSwapOperator.c:p5" intparameter="@rateCategories.c:p5" spec="SwapOperator" weight="10.0"/>
- <operator id="relaxedUpDownOperator.c:p3" scaleFactor="0.75" spec="UpDownOperator" weight="3.0">
- <parameter idref="ucldMean.c:p3" name="up"/>
- <tree idref="Tree.t:p3" name="down"/>
- </operator>
+ <operator id="narrow.t:p5" spec="Exchange" tree="@Tree.t:p5" weight="15.0"/>
- <operator id="ucldMeanScaler.c:p4" parameter="@ucldMean.c:p4" scaleFactor="0.5" spec="ScaleOperator" weight="1.0"/>
+ <operator id="treeScaler.t:p5" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p5" weight="3.0"/>
- <operator id="ucldStdevScaler.c:p4" parameter="@ucldStdev.c:p4" scaleFactor="0.5" spec="ScaleOperator" weight="3.0"/>
+ <operator id="wide.t:p5" isNarrow="false" spec="Exchange" tree="@Tree.t:p5" weight="3.0"/>
- <operator id="CategoriesRandomWalk.c:p4" parameter="@rateCategories.c:p4" spec="IntRandomWalkOperator" weight="10.0" windowSize="1"/>
+ <operator id="CategoriesRandomWalk.c:p5" parameter="@rateCategories.c:p5" spec="IntRandomWalkOperator" weight="10.0" windowSize="1"/>
- <operator id="CategoriesSwapOperator.c:p4" intparameter="@rateCategories.c:p4" spec="SwapOperator" weight="10.0"/>
+ <operator id="CategoriesUniform.c:p5" parameter="@rateCategories.c:p5" spec="UniformOperator" weight="10.0"/>
- <operator id="CategoriesUniform.c:p4" parameter="@rateCategories.c:p4" spec="UniformOperator" weight="10.0"/>
+ <operator id="WilsonBalding.t:p5" spec="WilsonBalding" tree="@Tree.t:p5" weight="3.0"/>
+
+ <operator id="SubtreeSlide.t:p5" spec="SubtreeSlide" tree="@Tree.t:p5" weight="15.0"/>
+
+ <operator id="Reheight.t:p5" spec="NodeReheight" taxonset="@taxonsuperset" tree="@Tree.t:p5" weight="80.652">
+ <tree idref="Tree.t:p5" name="genetree"/>
+ </operator>
+
+ <operator id="updown.p5" scaleFactor="0.75" spec="UpDownOperator" weight="17.16">
+ <parameter idref="birthRate.t:Species" name="up"/>
+ <parameter id="clockRate.c:p5" name="up">1.0</parameter>
+ <parameter idref="clockRate.c:p5" name="up"/>
+ <parameter idref="clockRate.c:p5" name="up"/>
+ <parameter idref="clockRate.c:p5" name="up"/>
+ <parameter idref="popMean" name="down"/>
+ <parameter idref="popSize" name="down"/>
+ <tree idref="Tree.t:p5" name="down"/>
+ <tree idref="Tree.t:p5" name="down"/>
+ </operator>
+
+ <operator id="treeRootScaler.t:p5" rootOnly="true" scaleFactor="0.5" spec="ScaleOperator" tree="@Tree.t:p5" weight="3.0"/>
+
+ <operator id="ucldMeanScaler.c:p4" parameter="@ucldMean.c:p4" scaleFactor="0.5" spec="ScaleOperator" weight="1.0"/>
<operator id="relaxedUpDownOperator.c:p4" scaleFactor="0.75" spec="UpDownOperator" weight="3.0">
<parameter idref="ucldMean.c:p4" name="up"/>
<tree idref="Tree.t:p4" name="down"/>
</operator>
- <operator id="ucldMeanScaler.c:p5" parameter="@ucldMean.c:p5" scaleFactor="0.5" spec="ScaleOperator" weight="1.0"/>
+ <operator id="ucldMeanScaler.c:p2" parameter="@ucldMean.c:p2" scaleFactor="0.5" spec="ScaleOperator" weight="1.0"/>
- <operator id="ucldStdevScaler.c:p5" parameter="@ucldStdev.c:p5" scaleFactor="0.5" spec="ScaleOperator" weight="3.0"/>
+ <operator id="relaxedUpDownOperator.c:p2" scaleFactor="0.75" spec="UpDownOperator" weight="3.0">
+ <parameter idref="ucldMean.c:p2" name="up"/>
+ <tree idref="Tree.t:p2" name="down"/>
+ </operator>
- <operator id="CategoriesRandomWalk.c:p5" parameter="@rateCategories.c:p5" spec="IntRandomWalkOperator" weight="10.0" windowSize="1"/>
+ <operator id="ucldMeanScaler.c:p3" parameter="@ucldMean.c:p3" scaleFactor="0.5" spec="ScaleOperator" weight="1.0"/>
- <operator id="CategoriesSwapOperator.c:p5" intparameter="@rateCategories.c:p5" spec="SwapOperator" weight="10.0"/>
+ <operator id="relaxedUpDownOperator.c:p3" scaleFactor="0.75" spec="UpDownOperator" weight="3.0">
+ <parameter idref="ucldMean.c:p3" name="up"/>
+ <tree idref="Tree.t:p3" name="down"/>
+ </operator>
- <operator id="CategoriesUniform.c:p5" parameter="@rateCategories.c:p5" spec="UniformOperator" weight="10.0"/>
+ <operator id="ucldMeanScaler.c:p5" parameter="@ucldMean.c:p5" scaleFactor="0.5" spec="ScaleOperator" weight="1.0"/>
<operator id="relaxedUpDownOperator.c:p5" scaleFactor="0.75" spec="UpDownOperator" weight="3.0">
<parameter idref="ucldMean.c:p5" name="up"/>
@@ -504,44 +574,70 @@
<parameter idref="birthRate.t:Species" name="log"/>
<log idref="YuleModel.t:Species"/>
<log id="TreeHeight.Species" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:Species"/>
- <log idref="treeLikelihood.p3"/>
- <log idref="treePrior.t:p3"/>
- <log id="TreeHeight.t:p3" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:p3"/>
+ <log idref="treeLikelihood.p2"/>
<log idref="treeLikelihood.p1"/>
<log idref="treePrior.t:p1"/>
<log id="TreeHeight.t:p1" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:p1"/>
- <log idref="treeLikelihood.p2"/>
- <log idref="treePrior.t:p2"/>
- <log id="TreeHeight.t:p2" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:p2"/>
<log idref="treeLikelihood.p4"/>
- <log idref="treePrior.t:p4"/>
- <log id="TreeHeight.t:p4" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:p4"/>
+ <log idref="treeLikelihood.p3"/>
<log idref="treeLikelihood.p5"/>
- <log idref="treePrior.t:p5"/>
- <log id="TreeHeight.t:p5" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:p5"/>
<parameter idref="ucldStdev.c:p1" name="log"/>
<log branchratemodel="@RelaxedClock.c:p1" id="rate.c:p1" spec="beast.evolution.branchratemodel.RateStatistic" tree="@Tree.t:p1"/>
- <parameter idref="ucldMean.c:p2" name="log"/>
- <parameter idref="ucldStdev.c:p2" name="log"/>
+ <log id="TreeHeight.t:p2" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:p2"/>
<log branchratemodel="@RelaxedClock.c:p2" id="rate.c:p2" spec="beast.evolution.branchratemodel.RateStatistic" tree="@Tree.t:p2"/>
- <parameter idref="ucldMean.c:p3" name="log"/>
- <parameter idref="ucldStdev.c:p3" name="log"/>
+ <log idref="treePrior.t:p2"/>
+ <parameter idref="ucldStdev.c:p2" name="log"/>
+ <log id="TreeHeight.t:p3" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:p3"/>
<log branchratemodel="@RelaxedClock.c:p3" id="rate.c:p3" spec="beast.evolution.branchratemodel.RateStatistic" tree="@Tree.t:p3"/>
- <parameter idref="ucldMean.c:p4" name="log"/>
- <parameter idref="ucldStdev.c:p4" name="log"/>
+ <log idref="treePrior.t:p3"/>
+ <parameter idref="ucldStdev.c:p3" name="log"/>
+ <log id="TreeHeight.t:p4" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:p4"/>
<log branchratemodel="@RelaxedClock.c:p4" id="rate.c:p4" spec="beast.evolution.branchratemodel.RateStatistic" tree="@Tree.t:p4"/>
- <parameter idref="ucldMean.c:p5" name="log"/>
- <parameter idref="ucldStdev.c:p5" name="log"/>
+ <log idref="treePrior.t:p4"/>
+ <parameter idref="ucldStdev.c:p4" name="log"/>
+ <log id="TreeHeight.t:p5" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:p5"/>
<log branchratemodel="@RelaxedClock.c:p5" id="rate.c:p5" spec="beast.evolution.branchratemodel.RateStatistic" tree="@Tree.t:p5"/>
+ <log idref="treePrior.t:p5"/>
+ <parameter idref="ucldStdev.c:p5" name="log"/>
+ <parameter idref="ucldMean.c:p4" name="log"/>
+ <parameter idref="ucldMean.c:p2" name="log"/>
+ <parameter idref="ucldMean.c:p3" name="log"/>
+ <parameter idref="ucldMean.c:p5" name="log"/>
</logger>
<logger fileName="species_$(seed).trees" id="speciesTreeLogger" logEvery="5000" mode="tree">
<log id="SpeciesTreeLoggerX" popSize="@popSize" spec="beast.evolution.speciation.SpeciesTreeLogger" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:Species">
<treetop id="treeTopFinder" spec="beast.evolution.speciation.TreeTopFinder">
- <tree idref="Tree.t:p3"/>
<tree idref="Tree.t:p1"/>
+ <tree idref="Tree.t:p4"/>
+ <tree idref="Tree.t:p2"/>
+ <tree idref="Tree.t:p3"/>
+ <tree idref="Tree.t:p5"/>
+ </treetop>
+ </log>
+ <log id="p21" popSize="@popSize" spec="beast.evolution.speciation.SpeciesTreeLogger" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:p2">
+ <treetop id="p22" spec="beast.evolution.speciation.TreeTopFinder">
+ <tree idref="Tree.t:p2"/>
<tree idref="Tree.t:p2"/>
+ <tree idref="Tree.t:p2"/>
+ <tree idref="Tree.t:p2"/>
+ </treetop>
+ </log>
+ <log id="p31" popSize="@popSize" spec="beast.evolution.speciation.SpeciesTreeLogger" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:p3">
+ <treetop id="p32" spec="beast.evolution.speciation.TreeTopFinder">
+ <tree idref="Tree.t:p3"/>
+ <tree idref="Tree.t:p3"/>
+ <tree idref="Tree.t:p3"/>
+ </treetop>
+ </log>
+ <log id="p41" popSize="@popSize" spec="beast.evolution.speciation.SpeciesTreeLogger" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:p4">
+ <treetop id="p42" spec="beast.evolution.speciation.TreeTopFinder">
+ <tree idref="Tree.t:p4"/>
<tree idref="Tree.t:p4"/>
+ </treetop>
+ </log>
+ <log id="p51" popSize="@popSize" spec="beast.evolution.speciation.SpeciesTreeLogger" speciesTreePrior="@SpeciesTreePopSize.Species" tree="@Tree.t:p5">
+ <treetop id="p52" spec="beast.evolution.speciation.TreeTopFinder">
<tree idref="Tree.t:p5"/>
</treetop>
</log>
@@ -554,22 +650,22 @@
<log idref="prior"/>
</logger>
- <logger fileName="$(tree).$(seed).trees" id="treelog.t:p3" logEvery="5000" mode="tree">
- <log branchratemodel="@RelaxedClock.c:p3" id="TreeWithMetaDataLogger.t:p3" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:p3"/>
+ <logger fileName="$(tree).$(seed).trees" id="treelog.t:p2" logEvery="5000" mode="tree">
+ <log branchratemodel="@RelaxedClock.c:p2" id="TreeWithMetaDataLogger.t:p2" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:p2"/>
</logger>
<logger fileName="$(tree).$(seed).trees" id="treelog.t:p1" logEvery="5000" mode="tree">
<log branchratemodel="@RelaxedClock.c:p1" id="TreeWithMetaDataLogger.t:p1" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:p1"/>
</logger>
- <logger fileName="$(tree).$(seed).trees" id="treelog.t:p2" logEvery="5000" mode="tree">
- <log branchratemodel="@RelaxedClock.c:p2" id="TreeWithMetaDataLogger.t:p2" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:p2"/>
- </logger>
-
<logger fileName="$(tree).$(seed).trees" id="treelog.t:p4" logEvery="5000" mode="tree">
<log branchratemodel="@RelaxedClock.c:p4" id="TreeWithMetaDataLogger.t:p4" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:p4"/>
</logger>
+ <logger fileName="$(tree).$(seed).trees" id="treelog.t:p3" logEvery="5000" mode="tree">
+ <log branchratemodel="@RelaxedClock.c:p3" id="TreeWithMetaDataLogger.t:p3" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:p3"/>
+ </logger>
+
<logger fileName="$(tree).$(seed).trees" id="treelog.t:p5" logEvery="5000" mode="tree">
<log branchratemodel="@RelaxedClock.c:p5" id="TreeWithMetaDataLogger.t:p5" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:p5"/>
</logger>
Regards, Cymon
Beth B
Nov 14, 2015, 12:04:07 PM11/14/15
to beast-users
Hi all,
I found the solution to the "Cannot find species for lineage ..." problem in *BEAST.
The problem occurs when the taxa trait names are the same as some of the species names. So give your traits different names to the species names and this problem gets solved.
Cheers,
Beth
Jim McGuire
Jan 4, 2016, 7:09:02 PM1/4/16
to beast-users
Did you get an answer to your question or otherwise resolve the issue?
I'm getting the same error message and trying to figure out if this is something I have done incorrectly with BEAUTI, which seems likely given that the tutorials are all out of date relative to this version.
Thanks!
Jim
java.lang.Exception: Cannot find species with name volans in species tree
at beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution.initAndValidate(Unknown Source)
at beast.util.XMLParser.initPlugins(Unknown Source)
at beast.util.XMLParser.parse(Unknown Source)
at beast.util.XMLParser.parseFile(Unknown Source)
at beast.app.BeastMCMC.parseArgs(Unknown Source)
at beast.app.beastapp.BeastMain.main(Unknown Source)
at beast.app.beastapp.BeastLauncher.main(Unknown Source)
Error 110 parsing the xml input file
validate and intialize error: Cannot find species with name volans in species tree
Error detected about here:
<beast>
<run id='mcmc' spec='MCMC'>
<distribution id='posterior' spec='util.CompoundDistribution'>
<distribution id='speciescoalescent' spec='util.CompoundDistribution'>
<distribution id='treePrior.t:Contig139' spec='beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution'>
logout
...
Jim McGuire
Jan 4, 2016, 7:15:36 PM1/4/16
to beast-users
Sorry - meant to reply to this message not that of Beth B..
Did you get an answer to your question or otherwise resolve the issue?
I'm getting the same error message and trying to figure out if this is something I have done incorrectly with BEAUTI, which seems likely given that the tutorials are all out of date relative to this version.
Thanks!
Jim
java.lang.Exception: Cannot find species with name volans in species tree
at beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution.initAndValidate(Unknown Source)
at beast.util.XMLParser.initPlugins(Unknown Source)
at beast.util.XMLParser.parse(Unknown Source)
at beast.util.XMLParser.parseFile(Unknown Source)
at beast.app.BeastMCMC.parseArgs(Unknown Source)
at beast.app.beastapp.BeastMain.main(Unknown Source)
at beast.app.beastapp.BeastLauncher.main(Unknown Source)
Error 110 parsing the xml input file
validate and intialize error: Cannot find species with name volans in species tree
Error detected about here:
<beast>
<run id='mcmc' spec='MCMC'>
<distribution id='posterior' spec='util.CompoundDistribution'>
<distribution id='speciescoalescent' spec='util.CompoundDistribution'>
<distribution id='treePrior.t:Contig139' spec='beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution'>
logout
On Wednesday, November 12, 2014 at 8:44:37 AM UTC-8, Cymon Cox wrote:
...
Mahwash Jamy
Jan 25, 2016, 10:21:36 PM1/25/16
to beast-users
Hi Jim (and everyone else),
Did you manage to resolve this issue?
I just loaded my data on Beauti v.2.3.3 using the *beast template -- set taxon sets and saved. I'm getting the same error message when I run this on Beast2.
Cheers,
Mahwash
janex...@gmail.com
Dec 30, 2016, 10:05:35 AM12/30/16
to beast-users
Hi Mahwash (and everyone else),
在 2016年1月26日星期二 UTC+8上午11:21:36，Mahwash Jamy写道：
I meet the same error, and figure it out by changing the same name of sequences and taxa, which has only one sequence. If your data are in similar case, please try this.
But the new running stopped at the following:
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)
I tried another seed, but it happened again.
Anyone met this before? Any suggestion? Thanks.
Happy new year!
Cheers
Jane
在 2016年1月26日星期二 UTC+8上午11:21:36，Mahwash Jamy写道：
mumm...@gmail.com
Mar 27, 2019, 5:42:13 AM3/27/19
to beast-users
Dear Beast Users:
在 2014年10月18日星期六 UTC+8下午9:10:11，James Worth写道：
I am trying to use multi-type birth-death model to analyse 3 location sequences,but it always show'validate and intialize error:4'
Thanks
Jin
在 2014年10月18日星期六 UTC+8下午9:10:11，James Worth写道：
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