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incorrect calculation of mutation rates U and V? #9

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mmatschiner opened this issue Sep 22, 2016 · 0 comments
Open

incorrect calculation of mutation rates U and V? #9

mmatschiner opened this issue Sep 22, 2016 · 0 comments

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@mmatschiner
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The "Calc mutation rates" button might calculate U and V incorrectly.
With the following alignment

NEXUS

begin data;
dimensions ntax=2 nchar=2;
format datatype=integerdata symbols="01" missing=- interleave=no;
matrix
spc1 11
spc2 01
;
end;

the resulting values are u=0.66666 and v=2.0, however u (according to help tip "Instantaneous rate of mutating from the 0 allele to the 1 allele") should be higher.

Results are also different when missing data is added. With the alignment

NEXUS

begin data;
dimensions ntax=2 nchar=4;
format datatype=integerdata symbols="01" missing=- interleave=no;
matrix
spc1 11--
spc2 01--
;
end;

the values are u=1.3333 and v=0.8.

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