Comments (6)
Perhaps the MRCAPriorWithRogues
is what you are looking for. It is in the BEASTLabs package. To use it requires a bit of XML editing. Probably easiest is to set up an MRCA prior in BEAUti and specify the taxa in taxonlist1
. Save the file, and open the XML in a text editor. Go to the MRCA prior, which looks something like this:
<distribution id="taxonlist1.prior" spec="beast.base.evolution.tree.MRCAPrior" tree="@Tree.t:dna" monophyletic="true">
<taxonset id="taxonlist1" spec="TaxonSet">
<taxon id="Carp" spec="Taxon"/>
<taxon id="Chicken" spec="Taxon"/>
<taxon id="Cow" spec="Taxon"/>
</taxonset>
</distribution>
Replace the spec attribute with beastlabs.math.distributions.MRCAPriorWithRogues
and add the rogues in taxonlist2, so it looks like this:
<distribution id="taxonlist1.prior" spec="beastlabs.math.distributions.MRCAPriorWithRogues" tree="@Tree.t:dna" monophyletic="true">
<taxonset id="taxonlist1" spec="TaxonSet">
<taxon id="Carp" spec="Taxon"/>
<taxon id="Chicken" spec="Taxon"/>
<taxon id="Cow" spec="Taxon"/>
</taxonset>
<rogues id="taxonlist2" spec="TaxonSet">
<taxon id="Dog" spec="Taxon"/>
<taxon id="Dolphin" spec="Taxon"/>
<taxon id="Duck" spec="Taxon"/>
</rogues>
</distribution>
You need to have to the BEASTLabs package installed to run the XML. Hope this is what you had in mind.
from beast2.
Dear Remco,
great, thanks so much! Of course that is exactly what we need.
However, now initialization apparently does not work anymore with the NJ starting tree. Is it possible that this function only works with hard constraints and not with such partial constraints?
Thanks a lot for your help,
Seraina
from beast2.
Hi Seraina,
The ClusterTree
indeed does not pick up such constraints, but the ConstrainedClusterTree
. Can you try replacing the XML element with spec="ClusterTree"
to spec="beastlabs.evolution.tree.ConstrainedClusterTree"
and see whether that starts.
Cheers, Remco
from beast2.
Dear Remco
Thank you already for your help. Seraina and I tried with the ConstrainedClusterTree, but now the analysis will not initialize because it detects negative branch lengths. Do you know what the issue could be? We tried already to use different seeds.
Best,
Alexandra
from beast2.
Hi Alexandra,
The ConstrainedClusterTree has a minimum branch length option (defaults to minBranchLength="1e-10"
) that should guarantee some minimum branch length. Obviously, this is not working for your analysis. If you can send me the XML I can have a look at what is causing the problem.
Have you tried using a RandomTree
for initialisation? This is recommended in general in order to not bias the MCMC sample by a fixed starting point.
Cheers, Remco
from beast2.
Dear Remco,
thanks so much for all your help - Alexandra is in the last weeks of her PhD, and your input already greatly helped us speed up the process!
We are now using both a random and a user tree as starting trees and compare the outcome. So currently, we have a work-around for the issue with the ConstrainedClusterTree (it is a dataset with a large number of highly incomplete fossils and thus a lot of uncertainty in the topology, which is making convergence very slow - hence our need to use a good starting tree as well).
But if it is interesting for you to get our input files in any case to repeat the issue, let us know. Otherwise, from our side, this could be closed.
Thanks again!
Seraina
from beast2.
Related Issues (20)
- Clarification about Trees and StateNodeInitialiser HOT 4
- TreeAnnotator does not respond to TargetTreeType in GUI
- BEAUti error importing alignment HOT 1
- error in parsing xml with no prior manual editing HOT 2
- .xml.state not found HOT 5
- Resume problem for monophyletic HOT 5
- Likelihood incorrectly calculated error HOT 5
- Hiccups with preparing package for testing HOT 1
- Make Alignment a StateNode
- no main manifest attribute on newer release
- Prep for v2.7.7 release
- Treeannotator not going to 100% HOT 1
- Remove jars when updating packages HOT 1
- Generate xml file in linux command line HOT 2
- Class (orc.consoperators.UcldScalerOperator) could not be found HOT 4
- Request a feature to use "version_file" in AppLauncher HOT 2
- Resuming from a state file does not update parameter dimensiom HOT 1
- When is a node's nodeNr ever greater than the root's nodeNr? HOT 1
- Add case to Tree.adjustTreeNodeHeights method to accommodate zero-length branches
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from beast2.