Skip to content

incorrect calculation of mutation rates U and V? #9

Description

@mmatschiner

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.

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Fields

    No fields configured for issues without a type.

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions