Fmatrix {DNAseqtest} | R Documentation |

## Joint Distribution for Two Matched Sequences

### Description

This function calculates the joint distribution function for two edge tree.

### Usage

`Fmatrix(t1, t2, f0, Sx2, Sy2, Pix, Piy)`

### Arguments

`t1` |
represents the length from the tree root to the first node |

`t2` |
represents the length from the tree root to the second node |

`f0` |
the initial distribution for the four nucleotides |

`Sx2` |
a 4 x 4 symmetric matrix related to the first edge |

`Sy2` |
a 4 x 4 symmetric matrix related to the second edge |

`Pix` |
a diagonal matrix for the stationary distribution of the first edge |

`Piy` |
a diagonal matrix for the stationary distribution of the second edge |

### Details

This function calculates the joint distribution function for a two edge tree with different edge lengths, stationary distributions and differentS matrices.

### Value

A 4 x 4 matrix containing the joint edges

### References

Faisal Ababneh, Lars S Jermiin, Chunsheng Ma, John Robinson (2006). Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences. Bioinformatics, 22(10), 1225-1231.

### See Also

gn, Smatrix

### Examples

```
f0<-c(.25,.25,.25,.25)
Pi1<-diag(c(.2,.2,.2,.4))
Pi2<-diag(c(.1,.1,.1,.7))
S1<-Smatrix(c(.2,.2,.2,.2,.2,.2),diag(Pi1))
S2<-Smatrix(c(.3,.3,.3,.3,.3,.3),diag(Pi2))
fm<-Fmatrix(1, .5, f0, S1, S2, Pi1, Pi2)
fm
```

*DNAseqtest*version 1.0 Index]