Description Usage Arguments Value Author(s) References See Also Examples

View source: R/dist.alignment.R

These functions compute a matrix of pairwise distances from aligned sequences using similarity (Fitch matrix, for protein sequences only) or identity matrix (for protein and DNA sequences). The resulting matrix contains the squared root of the pairwise distances. For example, if identity between 2 sequences is 80 the squared root of (1.0 - 0.8) i.e. 0.4472136.

1 | ```
dist.alignment(x, matrix = c("similarity", "identity"),gap)
``` |

`x` |
an object of class |

`matrix` |
the matrix distance to be used, partial matching allowed |

`gap` |
-optional- with nucleotides, if set to 1, gaps will be counted in the identity measure |

The distance matrix, object of class `dist`

, computed by using the
specified distance measure.

D. Charif, J.R. Lobry

The reference for the similarity matrix is :

Fitch, W.M. (1966) An improved method of testing for evolutionary homology.
*J. Mol. Biol.*, **16**:9-16.

`citation("seqinr")`

1 2 3 4 | ```
myseqs <- read.alignment(file = system.file("sequences/test.mase",
package = "seqinr"), format = "mase")
dist.alignment(myseqs, matrix = "identity" )
as.matrix(dist.alignment(myseqs, matrix = "identity" ))
``` |

```
Langur Baboon Human Rat Cow
Baboon 0.3307189
Human 0.3750000 0.3307189
Rat 0.5448624 0.5077524 0.5376453
Cow 0.4921255 0.5448624 0.5590170 0.6495191
Horse 0.7071068 0.7071068 0.7015608 0.7015608 0.7342088
Langur Baboon Human Rat Cow Horse
Langur 0.0000000 0.3307189 0.3750000 0.5448624 0.4921255 0.7071068
Baboon 0.3307189 0.0000000 0.3307189 0.5077524 0.5448624 0.7071068
Human 0.3750000 0.3307189 0.0000000 0.5376453 0.5590170 0.7015608
Rat 0.5448624 0.5077524 0.5376453 0.0000000 0.6495191 0.7015608
Cow 0.4921255 0.5448624 0.5590170 0.6495191 0.0000000 0.7342088
Horse 0.7071068 0.7071068 0.7015608 0.7015608 0.7342088 0.0000000
```

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