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Neighbor joining with phylogenetic diversity estimates | | Dan Levy
; Ruriko Yoshida
; Lior Pachter
; | | Date: |
30 Jul 2005 | | Subject: | Quantitative Methods; Combinatorics | q-bio.QM math.CO | | 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/ . | | Source: | arXiv, q-bio.QM/0508001 | | Services: | Forum | Review | PDF | Favorites | |
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