Ancestral Root Sequence

[man...@umich.edu]

Hello,

Please excused my ignorance, I am a novice to Beast and molecular phylogenetic. I am running Beast 2.5.0, and my main purpose is to determine the sequence of the root for a non-coding RNA gene tree. I previously stumbled upon the  Ancestor Sequence Rescue (https://github.com/armanbilge/AncestralSequenceRescue) discussed here https://groups.google.com/forum/#!topic/beast-users/jSeWxDTvts4. But the aforementioned thread indicates that 'Reconstruct states at all ancestors' option in Beauti must be marked before running beast. I can't seem to find such an option in Beauti 2. Is there a simple method to obtaining the root sequence in Beast 2? Any information would be helpful.

Thank you in advance.

 

[Remco Bouckaert]

There is no support in BEAUti 2 for reconstructing ancestral sequences, but if you install the BEASTLabs packaged, you can add the following logger in the XML (for example, just after where the other loggers are) to do so:

   <logger id="ancestral state" fileName=“rootstate.log" logEvery="1000">

        <log id="AncestralStateLogger" spec="AncestralStateLogger" data="@ringe" branchRateModel="@RelaxedClock.c:ringe" tree="@Tree.t:ringe" siteModel="@SiteModel.s:ringe">

            <taxonset idref=“TaxonSet.ringe”/>

        </log>

    </logger>

This is for a dataset called “ringe”, but you should edit it such that to point to the relevant items for your data, and make sure the clock model (here RelaxedClock.c:ringe) matches your clock model — if you use a relaxed clock, it is fine as is, but if you use another clock model you may need to edit it.

Cheers,

Remco

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[Matthew Manninen]

Thank you very much, Remco. 

On Mon, Jun 4, 2018 at 5:43 PM, Remco Bouckaert <higg...@gmail.com> wrote:

There is no support in BEAUti 2 for reconstructing ancestral sequences, but if you install the BEASTLabs packaged, you can add the following logger in the XML (for example, just after where the other loggers are) to do so:

   <logger id="ancestral state" fileName=“rootstate.log" logEvery="1000">

        <log id="AncestralStateLogger" spec="AncestralStateLogger" data="@ringe" branchRateModel="@RelaxedClock.c:ringe" tree="@Tree.t:ringe" siteModel="@SiteModel.s:ringe">

            <taxonset idref=“TaxonSet.ringe”/>

        </log>

    </logger>

This is for a dataset called “ringe”, but you should edit it such that to point to the relevant items for your data, and make sure the clock model (here RelaxedClock.c:ringe) matches your clock model — if you use a relaxed clock, it is fine as is, but if you use another clock model you may need to edit it.

Cheers,

Remco

On 5/06/2018, at 6:14 AM, man...@umich.edu wrote:

Hello,

Please excused my ignorance, I am a novice to Beast and molecular phylogenetic. I am running Beast 2.5.0, and my main purpose is to determine the sequence of the root for a non-coding RNA gene tree. I previously stumbled upon the  Ancestor Sequence Rescue (https://github.com/armanbilge/AncestralSequenceRescue) discussed here https://groups.google.com/forum/#!topic/beast-users/jSeWxDTvts4. But the aforementioned thread indicates that 'Reconstruct states at all ancestors' option in Beauti must be marked before running beast. I can't seem to find such an option in Beauti 2. Is there a simple method to obtaining the root sequence in Beast 2? Any information would be helpful.

Thank you in advance.

 

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