Fast computation of distance estimators

9 years 8 months ago
Fast computation of distance estimators
Background: Some distance methods are among the most commonly used methods for reconstructing phylogenetic trees from sequence data. The input to a distance method is a distance matrix, containing estimated pairwise distances between all pairs of taxa. Distance methods themselves are often fast, e.g., the famous and popular Neighbor Joining (NJ) algorithm reconstructs a phylogeny of n taxa in time O(n3). Unfortunately, the fastest practical algorithms known for Computing the distance matrix, from n sequences of length l, takes time proportional to l·n2. Since the sequence length typically is much larger than the number of taxa, the distance estimation is the bottleneck in phylogeny reconstruction. This bottleneck is especially apparent in reconstruction of large phylogenies or in applications where many trees have to be reconstructed, e.g., bootstrapping and genome wide applications. Results: We give an advanced algorithm for Computing the number of mutational events between DNA sequ...
Isaac Elias, Jens Lagergren
Added 09 Dec 2010
Updated 09 Dec 2010
Type Journal
Year 2007
Authors Isaac Elias, Jens Lagergren
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