R: Pairwise Distances from Sequences

dist.hamming {phangorn} | R Documentation

## Pairwise Distances from Sequences

### Description

`dist.hamming`, `dist.ml` and `dist.logDet` compute pairwise distances for an object of class `phyDat`. `dist.ml` uses DNA / AA sequences to compute distances under different substitution models.

### Usage

    dist.hamming(x, ratio = TRUE, exclude = "none")

    dist.ml(x, model = "JC69", exclude = "none", bf = NULL, Q = NULL,
      k = 1L, shape = 1, ...)

    dist.ml2(x, model = "JC69", exclude = "none", bf = NULL, Q = NULL,
      k = 1L, shape = 1, ...)

    dist.logDet(x)

### Arguments

`x` | An object of class `phyDat`
`ratio` | Compute uncorrected ('p') distance or character difference.
`exclude` | One of "none", "all", "pairwise" indicating whether to delete the sites with missing data (or ambiguous states). The default is handle missing data as in pml.
`model` | One of "JC69", "F81" or one of 17 amino acid models see details.
`bf` | A vector of base frequencies.
`Q` | A vector containing the lower triangular part of the rate matrix.
`k` | Number of intervals of the discrete gamma distribution.
`shape` | Shape parameter of the gamma distribution.
`...` | Further arguments passed to or from other methods.

### Details

So far 17 amino acid models are supported ("WAG", "JTT", "LG", "Dayhoff", "cpREV", "mtmam", "mtArt", "MtZoa", "mtREV24", "VT","RtREV", "HIVw", "HIVb", "FLU", "Blossum62", "Dayhoff_DCMut" and "JTT_DCMut") and additional rate matrices and frequencies can be supplied.

The "F81" model uses empirical base frequencies, the "JC69" equal base frequencies. This is even the case if the data are not nucleotides.

### Value

an object of class `dist`

### Author(s)

Klaus Schliep klaus.schliep@gmail.com

### References

Lockhart, P. J., Steel, M. A., Hendy, M. D. and Penny, D. (1994) Recovering evolutionary trees under a more realistic model of sequence evolution. Molecular Biology and Evolution, 11, 605–602.

Jukes TH and Cantor CR (1969). Evolution of Protein Molecules. New York: Academic Press. 21–132.

### See Also

For more distance methods for nucleotide data see `dist.dna` and `dist.p` for pairwise polymorphism p-distances. `writeDist` for export and import distances.

### Examples

    data(Laurasiatherian)
    dm1 <- dist.hamming(Laurasiatherian)
    tree1 <- NJ(dm1)
    dm2 <- dist.logDet(Laurasiatherian)
    tree2 <- NJ(dm2)
    treedist(tree1,tree2)
    # JC model
    dm3 <- dist.ml(Laurasiatherian)
    tree3 <- NJ(dm3)
    treedist(tree1,tree3)
    # F81 + Gamma
    dm4 <- dist.ml(Laurasiatherian, model="F81", k=4, shape=.4)
    tree4 <- NJ(dm4)
    treedist(tree1,tree4)
    treedist(tree3,tree4)

[Package phangorn version 2.6.2 Index]