dorsal/arxiv
View SchemaNeighbor joining with phylogenetic diversity estimates
| Authors | Dan Levy, Ruriko Yoshida, Lior Pachter |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0508001 |
| URL | https://arxiv.org/abs/q-bio/0508001 |
Abstract
The Neighbor-Joining algorithm is a recursive procedure for reconstructing trees that is based on a transformation of pairwise distances between leaves. We present a generalization of the neighbor-joining transformation, which uses estimates of phylogenetic diversity rather than pairwise distances in the tree. This leads to an improved neighbor-joining algorithm whose total running time is still polynomial in the number of taxa. On simulated data, the method outperforms other distance-based methods. We have implemented neighbor-joining for subtree weights in a program called MJOIN which is freely available under the Gnu Public License at http://bio.math.berkeley.edu/mjoin/ .
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"abstract": "The Neighbor-Joining algorithm is a recursive procedure for reconstructing\ntrees that is based on a transformation of pairwise distances between leaves.\nWe present a generalization of the neighbor-joining transformation, which uses\nestimates of phylogenetic diversity rather than pairwise distances in the tree.\nThis leads to an improved neighbor-joining algorithm whose total running time\nis still polynomial in the number of taxa. On simulated data, the method\noutperforms other distance-based methods.\n We have implemented neighbor-joining for subtree weights in a program called\nMJOIN which is freely available under the Gnu Public License at\nhttp://bio.math.berkeley.edu/mjoin/ .",
"arxiv_id": "q-bio/0508001",
"authors": [
"Dan Levy",
"Ruriko Yoshida",
"Lior Pachter"
],
"categories": [
"q-bio.QM",
"math.CO"
],
"title": "Neighbor joining with phylogenetic diversity estimates",
"url": "https://arxiv.org/abs/q-bio/0508001"
},
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