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ASR protein reconstruction and posterior probability of 1 #297

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kbaltazart opened this issue Mar 8, 2024 · 0 comments
Open

ASR protein reconstruction and posterior probability of 1 #297

kbaltazart opened this issue Mar 8, 2024 · 0 comments

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@kbaltazart
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I try to reconstruct ancestral sequence of protein. I use the parameters under (i cut protein for you to see better) :

begin data;
dimensions ntax=4 nchar=1057;
format datatype=protein missing=? gap=-;

matrix
[                                        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990       1000      1010      1020      1030      1040      1050    ]
[                                        .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .       ] 
Elephas_maximus_indicus			 QLSYGYDEKSAGGISV
Loxodonta_africana				 QLSYGYDEKSAGGISV
Mammut_americanum 				 QLSYGYDEKSAGGISV
Trichechus_manatus				 QLAYGYDEKSPGGISV
;

end;

begin mrbayes;
outgroup Trichechus_manatus;
prset aamodelpr=mixed;
constraint Elephantiforme -1 = 1 2 3;
constraint Elephantidae -1 = 1 2;
prset topologypr = constraints(Elephantidae, Elephantiforme);
report ancstates=yes;
mcmc nchains = 4 ngen=30000;
sumt;
sump;
end;

The program run and give me an output p.stats. However, the ancestral sequence for both clade is the same, with posterior probability of 1 for an amino-acid for a given site. The thing which is very strange is the fact that the ancestral sequence corresponds always to the last sequence in my matrice (even if it's the outgroup or not). I already tried to swap individuals, I have always an ancestral sequence corresponding to the last individual sequence.

Thank you for help.

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