| Title |
Provably Accurate Reconstruction of
Evolutionary Trees with Optimal Time and Space Complexities |
| Author(s) |
Ming-Yang Kao (This talk is based on joint work
with Miklos Csuros.) |
| Abstract |
Evolutionary trees are useful for modeling the
evolutionary history of organisms or species. An ultimate goal
of biology is to reconstruct the evolutionary history of all known
species. The determination of the evolutionary relationship of
all green plants alone will involve hundreds of millions of species.
Tree reconstructions of such scales require multidisciplinary
collaboration as well as enormous computational resources. While
we are not certain when, if ever, the necessary data will be ready,
DNA sequences of more and more species are becoming available.
In this talk, we will discuss a new algorithm for reconstructing
evolutionary trees from biomolecular sequences. In probabilistic
models of evolution, the algorithm is mathematically proven to
use sample sequences of length only polynomial in n to recover
the correct tree topology with high probability, where n is the
number of species involved. This accuracy guarantee is supported
by preliminary simulated experiments on the algorithm and its
variants. Given the pairwise distances between n input sequences,
the algorithm runs optimally in O(n^2) time using O(n) additional
work space in the worst case. Previously, the most popular distance-based
method, namely, Neighbor Joining, requires O(n^3) time and is
not known to have an accuracy guarantee. The other known polynomial-time
algorithms with accuracy guarantees take longer than O(n^3) time.
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