Description Usage Arguments Value Author(s)

`expand.distance.matrix`

updates a pairwise distance matrix with distances calculated between
the existing alignment and an additional sequence (assumed to be aligned)

1 2 | ```
expand.distance.matrix(aln, s, distmat = NULL, model = "TN93",
gamma = FALSE)
``` |

`aln` |
a multiple sequence alignment |

`s` |
a nucleotide sequence |

`distmat` |
a distance matrix (as a standard matrix). If |

`model` |
a model of nucleotide substitution (default=TN93) |

`gamma` |
the gamma parameter of rate variation |

A list with two elements: distmat, a distance matrix (as a standard R matrix), and aln, an updated alignment.

Simon Frost ([email protected])

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