Using Microsatellite loci for inferring one phylogenetic tree that uses all the loci

[Noa Chapal]

Hi,

I'm trying to use BEAST for phylogenetic tree reconstruction using microsatellite loci. Specifically, I have X taxa and Y microsatellite loci but some data is missing so each locus has signal in different sub-groups of the taxa (an example for such data is the example file microsatellite_data.txt located under examples\Data). 

I want to reconstruct a single tree which takes into account all the loci. Is it possible to perform such a task using BEAUti and BEAST? When I try to use the example file it produces separated trees for each locus. Is it possible to combine all the trees into one tree that uses all the loci?

Thank you,

Noa

[Noa Chapal]

Hi,

Someone has an answer?

Thanks

[Chieh-Hsi Wu]

Hi Noa,

 

Thank you taking an interesting the method.

 

Currently BEAUti won't let you link the trees for multiple loci msat data. This is because in the beginning when we added msat to BEAST the most important point was to have inferences incorporating the stochasticity in topology. We are curently making modifications to BEAUti so that it allows the trees to be linked for all loci and will let you know once that function has become available.

 

Kind regards,

 

Jessie

[Attila Csordas]

Hi Jessie,

is there any progress on linking multiple loci together for msat data in BEAST 1.x?

I tried to merge trees (Locus1.trees and Locus2.trees) from different loci together from the example distributed microsattelite.xml with LogCombiner v1.8.0 and got the following error:

Creating combined tree file: '/Applications/BEAST/examples/microsatellite/logcomb123mergetest'

Combining file: '/Applications/BEAST/examples/microsatellite/untitled.Locus1.trees' without removing burnin

Combining file: '/Applications/BEAST/examples/microsatellite/untitled.Locus2.trees' without removing burnin

Exception: Taxon, Locus2_2_T19, not recognized from first tree file

java.lang.IllegalArgumentException: Taxon, Locus2_2_T19, not recognized from first tree file

at dr.app.tools.LogCombiner.writeTree(Unknown Source)

at dr.app.tools.LogCombiner.writeTree(Unknown Source)

at dr.app.tools.LogCombiner.writeTree(Unknown Source)

at dr.app.tools.LogCombiner.writeTree(Unknown Source)

at dr.app.tools.LogCombiner.writeTree(Unknown Source)

at dr.app.tools.LogCombiner.writeTree(Unknown Source)

at dr.app.tools.LogCombiner.<init>(Unknown Source)

at dr.app.tools.LogCombiner.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)

Finished - Quit program to exit.

Would appreciate any help I have an actual problem I'm working on and need a solution,

Attila Csordas

EBI, UK

[Maryam]

Hi Jessie,

Currently, I am working on a microsatellite dataset and I am facing the same problem as Noa. I wanted to know If you have any progress in  modifications to BEAUti in order to address this issue?

Thanks so much,

Maryam

[Maryam]

Hi Jessie,

I am working on a microsatellite data and am facing the same problem as Noa. I wanted to know if you have any progress in a modification to BEAUTi to address this issue?

Thanks so much,

Maryam

[Maryam]

Hi,

I am using beast for inferring a phylogenetic tree from a microsatellite data, and am facing the same problem as Noa. I wanted to know if you have any progress in a modification to BEAUTi to address this issue?

Thanks,

Maryam

On Thursday, February 14, 2013 at 1:49:57 AM UTC-8, Noa Chapal wrote: