compevol / beast2

Bayesian Evolutionary Analysis by Sampling Trees

BEAST 2

BEAST is a cross-platform program for Bayesian inference using MCMC of molecular sequences. It is entirely oriented towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.

NOTE: This directory contains the BEAST 2 source code, and is therefore of interest primarily to BEAST 2 developers. For binary releases, user tutorials and other information you should visit the project website at beast2.org.

Development Rules and Philosophy

Aspects relating to BEAST 2 development such as coding style, version numbering and design philosophy are discussed on the BEAST 2 web page at beast2.org/package-development-guide/core-development-rules.

License

BEAST 2 is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. A copy of the license is contained in the file COPYING, located in the root directory of this repository.

This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License contained in the file COPYING for more details.

beast2's Issues

Path Sampling and/or Stepping Stone with BEAST2

Dear Walter,

Can you add this as an issue on BEAST2 google code site? The fix should be to automatically create the directory if it doesn't exist (and report doing so on the terminal).

Cheers
Alexei

Begin forwarded message:

Hi Yoshi,

The path sampler creates subdirectories, one for each step and the
rootdir='/tmp/step' in the example file specifies the locations of these
files. The error message you see indicates that the directory /tmp/step
does not exist on your computer.

You can either change the file and point rootdir to another location
that does exist on your computer -- and where you want the files to go.
Alternatively, you can create a /tmp/step directory on your computer.

Hope this helps,

Remco

Guess trait not correct

load nex (https://gist.github.com/tgvaughan/657cbfc3761e3fb7a009) and use *BEAST template, and guess trait. The XML in species part has wrong mapping (s0_tip11, s0_tip01) that are not existing in nex and BEASUti GUI.

            <taxonset id="taxonsuperset" spec="TaxonSet">
                <taxon id="s0" spec="TaxonSet">
                    <taxon id="s0_tip1" spec="Taxon"/>
                    <taxon id="s0_tip11" spec="Taxon"/>
                    <taxon id="s0_tip0" spec="Taxon"/>
                    <taxon id="s0_tip01" spec="Taxon"/>
                </taxon>
                <taxon id="s2" spec="TaxonSet">
                    <taxon id="s2_tip0" spec="Taxon"/>
                    <taxon id="s2_tip01" spec="Taxon"/>
                    <taxon id="s2_tip1" spec="Taxon"/>
                    <taxon id="s2_tip11" spec="Taxon"/>
                </taxon>
                <taxon id="s1" spec="TaxonSet">
                    <taxon id="s1_tip1" spec="Taxon"/>
                    <taxon id="s1_tip11" spec="Taxon"/>
                    <taxon id="s1_tip0" spec="Taxon"/>
                    <taxon id="s1_tip01" spec="Taxon"/>
                </taxon>
                <taxon id="s3" spec="TaxonSet">
                    <taxon id="s3_tip1" spec="Taxon"/>
                    <taxon id="s3_tip11" spec="Taxon"/>
                    <taxon id="s3_tip0" spec="Taxon"/>
                    <taxon id="s3_tip01" spec="Taxon"/>
                </taxon>
                <taxon id="s4" spec="TaxonSet">
                    <taxon id="s4_tip1" spec="Taxon"/>
                    <taxon id="s4_tip11" spec="Taxon"/>
                    <taxon id="s4_tip0" spec="Taxon"/>
                    <taxon id="s4_tip01" spec="Taxon"/>
                </taxon>
            </taxonset>

Refactor TreeLikelihood to allow variable number of partitions

Idea for an enhancement that would allow substbma and similar sitemodels to be just sitemodels, rather than also implementing their own TreeLikelihoods.

son of magic code in initAndValidate

I see this code in ClusterTree.java

public void initAndValidate() throws Exception {

    if (Boolean.valueOf(System.getProperty("beast.resume")) &&
                (isEstimatedInput.get() || (m_initial.get() != null && m_initial.get().isEstimatedInput.get()))) {
   ...
}

Is that the best we can do for beast2 implementers?
If so, it should be prominently documented (I was not aware of this issue until now).
It would be nice if the code knew not to call the initAndValidate on resume, or maybe just the parts that matter? Perhaps we can separate the init into two parts (first-time and resume)? or at least pass a flag in?

Resume should be robust to (small) differences in final state of log and trees file

What steps will reproduce the problem?

1. Terminate BEAST prematurely
2. Attempt to resume

What is the expected output? What do you see instead?

Resumption of MCMC expected, instead failure to resume can sometimes occur:
Error message from Thomas Vignaud:

Start likelihood: -7892.4621158294585
java.lang.Exception: Error 400: Cannot resume: log files do not end in same sample number
at beast.core.Logger.openLogFile(Unknown Source)
at beast.core.Logger.init(Unknown Source)
at beast.core.MCMC.run(Unknown Source)
at beast.app.BeastMCMC.run(Unknown Source)
at beast.app.beastapp.BeastMain.(Unknown Source)
at beast.app.beastapp.BeastMain.main(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at apple.launcher.LaunchRunner.run(LaunchRunner.java:116)
at apple.launcher.LaunchRunner.callMain(LaunchRunner.java:51)
at apple.launcher.JavaApplicationLauncher.launch(JavaApplicationLauncher.java:52)

Beast v2.0.2 / Reconstruction of ancestral state/ Improper handling of missing data?

Hi guys,

First of all, congratulations to the fabulous work done with the new version of Beast... Every time I come back to analyses after a few months of field or lab work, I am amazed by new developments...

Just a comment, I tried to link a morphological character to a species tree (in a *Beast framework)... and it seems that Beauty always creates a new state for missing data (I code them using question marks)... I indeed get this:

<userDataType codeMap="?=0,no=1,yes=2,? = 0 1 2 " codelength="-1" id="traitDataType.crenulated" spec="beast.evolution.datatype.UserDataType" states="3"/>

I tried to edit the xml by replacing the above code by:

<userDataType codeMap="no=0, yes=1, ? = 0 1" codelength="-1" id="traitDataType.crenulated" spec="beast.evolution.datatype.UserDataType" states="2"/>

And I also updated dimensions in the substitution model...

But it generates an error from the Beast:
"Error 110 parsing the xml input file
validate and intialize error: Could not find code ? in codemap"

Am I missing something?

Proper handling of missing data is important to me, because I often (need) exclude the outgroup state from the analysis...

Thanks in advance!

Additional comments from GC issue

Sep 1, 2013
Project Member #1 dong.w.xie

it needs further investigation to see if this is duplicated to issue #37

Refactoring of TreeParser

TreeParser is rather too complex and has a very large number of interacting Inputs. It should be rationalised, perhaps by introducing a subclass. One key distinction is whether the labels in the Newick tree are considered to be node numbers of labels. For example, this could be separated into a superclass that only handles numbers and a subclass that handles labels.

TreeParser should also have an option for single-child nodes of either reading them in as single-child nodes (i.e. for purposes of beast-graphics or TreeStat2) or as two-child nodes with a zero branch to labelled child (i.e. for BEAST MCMC of sampled ancestor trees).

release for Mac OS X 10.8

detail at email "Bundling Java apps for 10.8+"

Stochastic target distributions

There are a number of MCMC algorithms (eg BDSIR, PMMH) which employ stochastic integration to estimate a component of the target distribution. While it is possible to implement these schemes within the current BEAST framework, it isn't particularly easy.

For instance, in BDSIR the stochastic component is the tree likelihood, which requires simulation of a new epidemic trajectory whenever new epidemiological parameters are proposed. Denise has had to implement this by making the trajectory an explicit component of the state and creating a special wrapper operator around each of the parameter operators which updates this state whenever the parameters are modified.

A far easier approach would be to have the likelihood perform the trajectory simulation itself and keep the trajectory out of the state entirely. However, doing this currently results in BEAST errors due to the fact that the likelihood consistency checks fail.

It would therefore be handy to be able to switch this check off for particular calculation nodes marked as "stochastic". This isn't completely trivial, as the existing consistency check involves marking all state nodes as dirty and propagating this dirtiness through the calculation node dependency graph. It's therefore the dirtiness propagation that needs modifying in the particular instance that the dirtiness is due only to the consistency check.

FInalize implementation of Sampled Ancestor Trees

Choose whether to add new methods to Tree class or add subclass SampledAncestorTree.

New BEAUti should import data partitions from BEAST 1.x files

A minimum amount of parsing ability is required to extract taxa, sequences, dates and attributes from the XML files of BEAST 1.x. An importer for these is already available in dr. app.beauti.utils.

This would be a great benefit for the transition between versions.

Development of InputEditor in BEAUti2 to handle Matrices

This development involves building a Swing editor for Matrix parameters to allow easy input of initial values in BEAUti 2. Especially useful for SubstBMA plugin, but should be of general value.

BEAUti cannot handle big number of loci

I tested that BEAUti has problem to run when the number of loci > 128 or 256.

Some users also report this, especially for *BEAST: https://groups.google.com/forum/#!topic/beast-users/HsifLjGyXfg

We discussed this in the meeting, but it seems not logged.

NEXUS parser is incomplete

The Nexus parser (beast.util.NexusParser) only handles a minimum subset of the Nexus format. I suggest we switch to the JEBL nexus parser which is much more complete (handles Taxa and Characters blocks etc.). The wrapper class beast.app.beauti2.util.BeautiParser shows how to use this to load multiple partitions from a nexus file.

Make adding clades more obvious in Beauti

Perhaps there is a way to make addition of clades for calibration more obvious?

I missed the small '+' button in the Priors panel.

New operators needed to simultaneously change rates during tree operators with relaxed clock

The rates should be changed so as to keep the involved branch lengths in substitutions constant or near-constant after operation. Good luck with Hastings ratio.

plugins (aka addons) versioning

I tried running the latest version of Beauti with an old version of the RBS addon.

This resulted in an exception, and no user level error message.

Would be nice to have some versioning information which enable Beauti to detect this on startup and issue a sane, user-level warning or failure.

update BEAUti and wiki to use term "Package"

This is related to issue 32 .

I have replaced most of "Add-on(s)" into "Plugin(s)" in wiki, except of 2 wiki pages that contain GUI screenshots and user guide:

1. Writing an Add-on
2. Manage Add-ons

BEAUti 2 needs to be updated first, before these 2 pages can be re-written.

Walter

Additional comments from GC issue

Sep 13, 2013
Project Member #1 alexei.drummond

I prefer "Package" to "Plugin". Package sounds like something you could write a paper about and be proud of (as with an R package).

Once we decide on the right name, it should be applied everywhere, not piecemeal.

Sep 22, 2013
Project Member #2 alexei.drummond

(No comment was entered for this change.)

Refactoring Alignment to become an interface

Refactoring to allow flexibility in data representation.

resume fail with OutOfMemoryError while appending to tree log

I start with the largest possible -Xmx my 32bit cpu/java allows on my laptop. The trees file "only" 340M, and Remco says he successfully resumed larger files.

The file can be downloaded from
https://dl.dropboxusercontent.com/u/5675908/conus-al.tar.bz2

java -ea -Xmx2500m -Xss2024k -jar ... -seed 666 -resume conus-al.xml

...
Start likelihood: -30613.211722592572
Appending file conus-al.log
Sample posterior ESS(posterior) likelihood prior
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at java.util.Arrays.copyOf(Arrays.java:2882)
at java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:100)
at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:390)
at java.lang.StringBuilder.append(StringBuilder.java:119)
at beast.core.Logger.openLogFile(Unknown Source)
at beast.core.Logger.init(Unknown Source)
at beast.core.MCMC.run(Unknown Source)
at beast.app.BeastMCMC.run(Unknown Source)
at beast.app.beastapp.BeastMain.(Unknown Source)
at beast.app.beastapp.BeastMain.main(Unknown Source)

Allow linking of GTR rate parameters in BEAUti

The user should be able to link parameters in the prior panel like rateAC and rateAT parameters.

"Null pointer exception" on resume

An init node in the state without an ID seems to run fine, but cause a mysterious "Null pointer exception" on resume.

If this is really serious, the program should be flagged as bad before running?

Comments on GC issue

Project Member #1 higgs.ml

Init nodes should not pass on their ID to the node they initialise.

Status: Accepted
Labels: -Priority-Medium Priority-High
Oct 8, 2013
Project Member #2 higgs.ml

This might be fixed with the new implementation of storeToFile using JSON.

More magic in initAndValidate

Some plugins (RandomTree, CalibratedYuleModel, maybe others) pluck inputs from the prior (with what looks to me like risky code) or from their outputs.

It is not clear to me how this information is supposed to reach users who wish to modify the XML or even developers which may miss the code.

Should we really design plugins this way? I thought the whole idea in having "inspectable" inputs was to eliminate magic.

(I scratched my head in disbelief several times when I removed the inputs to RandomTree from the XML, yet they appeared in the debugger)

Parameter / Tree to become interfaces

This design change will allow for future developments including:

(1) Wrappers of Tree for use in tree prior calculations (i.e. NormalizedTree for Jessie Wu's substitution model averaging plugin)

(2) CompoundParameters that are made up of multiple parameters (including random numbers of parameters).

Comments on GC issue:

Project Member #4 alexei.drummond

I have completed the Parameter part of this issue. Actually the two parts are quite separate, so probably should have been two issues.

Status: Started
Sep 30, 2013
Project Member #5 higgs.ml

Dilemma: CompoundParameters either have a type, since Parameters are identified by their type, and each type can have its own interface --
RealParamterInterface, IntegerParameterInterface, etc. -- or we do away with all typed parameters. Is there another way?

Currently, very few Parameter-Inputs are available, most of them are typed parameter inputs, so a generic CompoundParameter is not very useful yet.

Oct 2, 2013
Project Member #6 alexei.drummond

Not sure what comment #5 is about? Parameter has already been changed to an interface... are more interfaces needed?

Oct 2, 2013
Project Member #7 higgs.ml

Imagine a CompoundParameter and an Operator that works on that CompoundParameter, say a ScaleOperator. Scaling only works with RealParameters, so it has a Input as an Input. To change this to CompoundParameter, either CompoundParameter has to

1. derive from RealParameter, but then the CompounParameter is a StateNode with RealParameters as inputs
2. CompoundParameter and RealParameter derive from RealParameterInterface, which gives one interface for each type
3. Change Input to Input in ScaleOperator and check the type

Any other solutions?

Oct 2, 2013
Project Member #8 alexei.drummond via email

Option 3 the nicest, no?

Oct 2, 2013
Project Member #9 higgs.ml

If we go for Option 3, we miss out on type safety, which means we could amalgamate RealParameter, IntegerParameter and BooleanParameter into Parameter.

Port microsatellite models to BEAST2

Port Jessie Wu's microsatellite models in BEAST1 to BEAST2

Error and Warning reporting in initAndValidate

CalibratedYuleModel.initAndValidate() contains this code

if (!_MRCAPrior.isMonophyleticInput.get()) {
  throw new Exception("MRCAPriors must be monophyletic for Calibrated Yule prior");
}

and

 if (_MRCAPrior.isMonophyleticInput.get()) {
    System.err.println("WARNING: MRCAPriors must have a distribution when monophyletic for Calibrated Yule prior");
}

I hope the exception is caught by BEAST2 and passed in a nicer way to the user (but not sure).

But the System.err.println looks bad to me. How does a plugin issues a warning? I think We need a system wide facility.

Comments on GC issue

Project Member #2 higgs.ml

Is this an error condition or should this be treated as warning?

Sep 29, 2013
Project Member #3 jheled

Since I can't remember adding this part of the code, I am assuming it is one of your additions. I would rather not have any of this "magic" and always require the calibration points to be specified explicitly.

My report was more on the topic of error reporting by a plugin.
A user may want to add other monophyly constraints. This breaks the prior guarantee, but the code can still run, so my guess it is just a warning.

Error 110 parsing the xml input file: Cannot find taxon MyTAXON in data

Hey Carlos,

Yes... that is a bug in Beauty I think... I got the same issue... It creates new elements using "id" (and adds 1 to pre-existing taxa names) instead of referring directly to those using "idref"

In my case I had to replace:

                <taxonset id="Ingroup" spec="TaxonSet">
                    <taxon id="aiensis1" spec="Taxon"/>
                    <taxon id="cynocephalus1" spec="Taxon"/>
                    <taxon id="eudentatus1" spec="Taxon"/>
                    <taxon id="franouxi1" spec="Taxon"/>
                    <taxon id="hageni1" spec="Taxon"/>
                    <taxon id="japonicus1" spec="Taxon"/>
                    <taxon id="lagocephalus1" spec="Taxon"/>
                    <taxon id="lenguru1" spec="Taxon"/>
                    <taxon id="lividus1" spec="Taxon"/>
                    <taxon id="longifilis1" spec="Taxon"/>
                    <taxon id="marquesensis1" spec="Taxon"/>
                    <taxon id="ouwensi1" spec="Taxon"/>
                    <taxon id="pugnans1" spec="Taxon"/>
                    <taxon id="punctissimus1" spec="Taxon"/>
                    <taxon id="rapa1" spec="Taxon"/>
                    <taxon id="sarasini1" spec="Taxon"/>
                    <taxon id="spBIF1" spec="Taxon"/>
                    <taxon id="stimpsoni1" spec="Taxon"/>
                    <taxon id="stiphodonoides1" spec="Taxon"/>
                </taxonset>

by this

                <taxonset id="Ingroup" spec="TaxonSet">
                    <taxon idref="aiensis"/>
                    <taxon idref="cynocephalus"/>
                    <taxon idref="eudentatus"/>
                    <taxon idref="franouxi"/>
                    <taxon idref="hageni"/>
                    <taxon idref="japonicus"/>
                    <taxon idref="lagocephalus"/>
                    <taxon idref="lenguru"/>
                    <taxon idref="lividus"/>
                    <taxon idref="longifilis"/>
                    <taxon idref="marquesensis"/>
                    <taxon idref="ouwensi"/>
                    <taxon idref="pugnans"/>
                    <taxon idref="punctissimus"/>
                    <taxon idref="rapa"/>
                    <taxon idref="sarasini"/>
                    <taxon idref="spBIF"/>
                    <taxon idref="stimpsoni"/>
                    <taxon idref="stiphodonoides"/>
                </taxonset>

Additional comments on GC issue

Project Member #1 higgs.ml

What should be done to reproduce this one?

Remco

Document and clean up code

Add comments to code that is not obvious, rename variables to conform to Java naming standard, and generally clean up code

unit test for ScaleOperator

add a unit test that tests that the ScaleOperator correctly scales a tree

Improve the starting state for *BEAST analyses with a large number of loci (i.e. >= 8 loci)

Joseph has devised a new heuristic for creating a starting state for a *BEAST analysis when there are a large numbers of loci. We should incorporate this into the *BEAST state initialisation in BEAST2 to avoid very long burn-in times with large analyses.

Comments from GC issue

Project Member #1 jheled

Code submitted, tested lightly. Needs more testing, and integration with templates and BEAUTI.

separated library path for different version

Error: cannot use beast 2.0.2 after installed 2.1.0 packages.

All versions are using the same library path.

We should create one sub-folder named by version number for each version, such as /Library/Application Support/BEAST/2.1.0/.

an error of # taxa is not equal to dimension

Hi Walter

I have run into another problem while using Beauti2.

When I try to import the attached nexus file, I get an error saying # taxa is not equal to dimension.
However, the same file works perfectly well in Beauti 1.75.
Any help would be appreciated.

Regards,

Alex

Additional comments from GC issue

Sep 29, 2013
Project Member #1 higgs.ml

This happens when the number of sequences found in the nexus file does not equal the number specified in the NEXUS dimensions block, e.g.

DIMENSIONS NTAX =26 NCHAR=614;

This should at least result in a warning, since it may be the alignment is malformed.

Do we have an example nexus file to reproduce this?

Remco

*BEAST + phylogeography has taxa missing

What steps will reproduce the problem?

1. start *BEAST analysis
2. add phylogeography trait

What is the expected output? What do you see instead?

Expected to be able to specify location for taxa.
There is only a single dummy taxon.
Needs to make all taxa in species tree available.

Document release procedure

So Remco can divulge himself of the duty.

Investiage alternatives to Swing

Swing based GUI development is specialised work and tedious.

E.g. try to implement the equivalent of this in Swing:

<button value='Click me' onclick='alert("Hello world")'>

This is a hinderance for BEAUti template developemnt, which rarises the question: is there a better way to develop/extend BEAUti. One alternative is JavaFX, another HTML/Javascript/CSS.

Beauti 2.0.2 not accepting .nex file

Reported by shvetanks, Jun 12, 2013

What steps will reproduce the problem?

1. Clustal Omega (EBI server) aligned file saved as .nex in Clustalx reports error "Something went wrong importing the alignment: Around line 2549
   Unknown code found in sequence: X"
2. There is no X sequence.
3. Same file works fine in Beauti1.7.5

What is the expected output? What do you see instead?

File should be listed in Partitions with details of sequences. Instead the following error shows- "Something went wrong importing the alignment:
Around line 2549
Unknown code found in sequence: X"

What version of the product are you using? On what operating system?

Error in Beauti 2.0.2 on Mac OSX 10.8.3

Please provide any additional information below.

This is an amino acid multiple alignment file.
Changing the extension to .nex or .nexuss after conversion does not help

Additional comments from GC issue

Sep 11, 2013
Project Member #1 dong.w.xie

Could you please attach the example of nex file? I cannot replicate using our example.

Thanks,
Walter

Relative operator weights

Relative operator weights would make life easier for *BEAST implementers.

My proposal is straightforward.

Note: not valid beast2 XML, but you get the idea

<operator weight="10">
  <operator name="op1" weight="2"/>
  <operator name="op2" weight="1"/>
</operator>

<operator name="op3" weight="5">

This is equivalent to the weights (10/15 * 2/3),(10/15 * 1/3) for op1/op2 and 5/15 for op3.

Basically, the total sum of all operators grouped together is equal to the weight of the group. It would be nice to have a democratic default:

<operator weight="10">
  <operator name="op1"/>
  <operator name="op2"/>
</operator>

is equivalent to a weight of 5 for both.

Comments from GC issue

Project Member #1 higgs.ml

Note, these meta-operators need care to store/restore from file (when resuming).

Sep 30, 2013
Project Member #4 higgs.ml

Issue 20 has been merged into this issue.

Cc: jheled
Oct 8, 2013
Project Member #5 higgs.ml

support for nested operator info in state file is now available

beauti parameter value editing

When editing a value of a parameter -- which is a list of primitives -- in the init panel, nothing suitable is found. A table editor matching dimensions would be nice.

Drag drop support for BEAUti in Windows is failing

User report "Is there any reason that the “drag-and-drop” method of importing alignments into BEAUti has gone away? I find this really handy as I’m selecting from a giant folder with hundreds of NEX files. Perhaps this feature could be returned in a future bug fix."

magic code in initAndValidate

The initAndValidate() for the CalibratedYuleModel class contains this code:

        if (nCals == 0) {
            // assume we are in beauti, back off for now
            return;
        }

Is this really the best BEAST2 can do for developers. How can a developer know if this magic is needed, and where? if there is no alternative, this must be very prominently and thoroughly documented.

Tip date sampling with individual priors

Hi everyone

Is there a possibility to perform tip date sampling with individual priors in the Beast2 package? I know this option from Beauti 1.7.5. In Beauti2 however, it seems to me that I can only give the same prior distribution to all samples within a taxon set.

Thanks for your help
Amelie

Add Merge button next to Split button on partition panel

So that partitions can be merged as well as split. For example the examples/primates-mtDNA.nex has 5 partitions specified, but in some instances you may want to just combine the partitions into a single one if you are using a single model, and linking them would not compress the patterns fully.

Newick tree is wrong

input original tree below into newick tree TreeParser, and then BEAST 2 output a different tree as inputted.

BEAST 2 output:
0.036831999999999976,1217:(615:(613:(612:(611:(2:0.0,3:0.006647999999999987):0.09753100000000003

input:
0.036831999999999976,(((('NZAC03011539|Plot_4|Subplot_P|LBIinv0013|G6|MT-CO1':0.0,'NZAC03013498|Plot_5|Subplot_A|LBIinv0012|B2|MT-CO1':0.006647999999999987):0.09753100000000003,

the number of brackets increased from 4 to 5.

original tree is attached.

Comments from GC issue

Project Member #1 alexei.drummond

Not sure this is a bug with TreeParser class. We should focus on issues with BEAST2, rather than code that uses BEAST2 classes.

Status: New
Labels: -Priority-High Priority-Low

Port model averaging of relaxed clock models from beast1 to beast2

Port Sibon Li's model averaging of relaxed clock models from beast1 to beast2

Assorted BEAUti enhancements

1. When you have a large number of genes, there's no scrolling in the gene list on the Site Model or Clock Model tabs. I had to flip my monitor to a portrait orientation to see the full list of 50 genes so that I could proceed.
2. In BEAUti v1.8 there is a "clone settings" function in the Site Model (or equivalent) tab. I couldn't see a similar functionality in v2.1.1., but it would be useful.
3. Similarly, in BEAUti v1.8 you can easily apply a rate to all genes using the "Clock Model Group" box in the Clocks tab. As best as I can tell, there's no similar functionality on the v2.1.1 Clock Model tab.
4. In the BEAUti v2.1.1. Priors tab, each time you select or modify a prior the view/cursor jumps back to the top of the list.
5. Also in the Priors tab, when you try to modify a prior which already has a value, that value gets duplicated. I was trying to add upper and lower bounds to my ucldMean priors. I had already set the clock rate in the Clock Model tab (1.0E-8) and when I tried to select the values to add the upper/lower bound this value would be duplicated on the screen. I confirmed that it was also duplicated in the XML file. In the end I added the upper/lower bound in the XML file using the ucldMean.c:Acpp entry to locate the area of the XML with this prior. It's probably easier to look at the attached screen capture to see what I mean.
6. Another from the Priors tab, should there be descriptions in every row? The descriptions seemed sort of haphazard - present for some parameters but not for most.
7. In the MCMC tab, if you want to change the interval of data logging, do you have to manually do that for each parameter (e.g., it seems like you need to change "Store Every" at the top and then "Log Every" for each parameter.

Error generating XML file with BEAUTi 2

Hi Walter

I was following the Phylogeography example that is on the BEAST2 page. I installed the add-ons BEAST_CLASSIC and BEASTii. I then click the + at the bottom left of the partition tab and choose to add continuous geography. I use this to enter the latitude and longitude for my samples.

When I followed this for the phylogeography example (raccoon rabies virus I believe) it worked fin and I could save the XML file.

Regards,

Alex

Additional comments on GC issue

Project Member #1 dong.w.xie

Hi Walter

I fixed the problem, it seemed to be occurring because I was using & to seperate groups.
When I changed all instances of & to _ it saved without any errors.

Regards,

Alex Stuckey

BEAUti Template for SubstBMA plugin

This is a crucial development to allow SubstBMA plugin (published in 2012) to be used/cited in BEAST2.

Comments from GC issue:

Project Member #3 higgs.ml

subst-bma plugin needs to be compilable

Oct 2, 2013
Project Member #4 alexei.drummond

Subst-bma compiles against BEAST2.0.2 -- if BEAST2.1 has changed the API such that subst-bma doesn't compile then I guess this issue depends on first changing it so it compiles again?

Oct 2, 2013
Project Member #5 higgs.ml

That is what I would expect.
If you foresee any development for v2.0.2, just branch off in SVN for that version only.

More detailed user error message

Print out the full name of the plugin in an error message, since two plugins with the same name may exist (like Uniform and Uniform, distribution and operator)

RandomTree.initAndValidate() calls its own initStateNodes()

RandomTree.initAndValidate() calls its own initStateNodes()

Seems like a wasted action, since initStateNodes() is called from the main initialization code.

For an addon, can we make the default for ant 'ant addon'

I tried a plain 'ant' and got into trouble, which might have been avoided if the default was 'addon'

(but maybe this is not possible??)

Comments from GC issue

Project Member #1 higgs.ml

This is more an issue for addons than for the core?
Not sure what can be done in the core to fix this.

Sep 29, 2013
Project Member #2 jheled

Perhaps we need to separate core issues and non-core issues?

As far as I understand, this issues list is for the whole of beast2 and not just the core.

I am assuming we will have a detailed example and/or documentation on how to build an addon (AKA the new plugin), and I was hoping the default there would be 'ant addon'