URGENT: Need more info: Ancestral sequence reconstruction

[LysSanzMoreta]

Hi!

I am trying to reconstruct a sequence for every node in the tree. I have been following the manual the best I could and I only get 1 sequence as an output when parsing it out. I use this inside my nexus file:

begin mrbayes;

    [This block defines several different character sets that could be used in partitioning these data
    and then defines and enforces a partition called favored.]

    set autoclose=yes nowarn=yes;
    lset nst=6 rates=invgamma ngammacat=4; [GTR+I+G model]
    prset ratepr=variable;
    taxset MyTaxset = A1 A2 A3 A4 A5 A6 A7 A8 A9 A10; **--> Does this mean that it will reconstruct the ancestor from all these nodes?**
    constraint MyConstraint = MyTaxset;
    prset topologypr = constraints(MyConstraint);
    report ancstates=yes;
    mcmc nruns=1 nchains=1 ngen=50000 checkpoint=no; 
    sump;
    quit;

end;

I am not sure about:

a) Do I need to give a tree topology as well somehow? I have a predefined tree topology

b) How to use taxset, constraint and topology in the right manner to obtain all the ancestral nodes.

c) Taxset says that it caanot be given more than 30 taxon names....what if I have 50 leaves and therefore 50 ancestral nodes?Am I constrained to small datasets?

Thank you very much in advance for your help!

[zhangchicool]

From "help report": Ancstates -- If this option is set to 'yes', MrBayes will print the pro-
bability of the ancestral states at all constrained nodes. Typ-
ically, you are interested in the ancestral states of only a few characters and only at one node in the tree. To perform such
an analysis, first define and enforce a topology constraint
using 'constraint' and 'prset topologypr = constraints (...)'.
Then put the character(s) of interest in a separate partition and set MrBayes to report the ancestral states for that partition.
For instance, if the characters of interest are in partition 2,
use 'report applyto=(2) ancstates=yes' to force MrBayes to print the probability of the ancestral states of those characters at
the constrained node to the '.p' file.
You may try following this procedure to see if it works.

[LysSanzMoreta]

Thanks, I can try to investigate the .p file in the output, because the rest seems the same as I did

[nylander]

No feedback since last message. Seems to be OK? Closing issue. Feel free to reopen if needed.