Sagot
Marie-France
en
2011
chapter
chapters
https://scigraph.springernature.com/explorer/license/
2019-04-16T09:10
2011-01-01
Recently, we have identified a quartet phylogeny algorithm with O(n logn) expected runtime, which is asymptotically optimal. Regardless of the true topology, our algorithm has high probability of returning the correct phylogeny when quartet errors are independent and occur with known probability, and when the algorithm uses a guide tree on O( loglogn) taxa that is correct with high probability. In practice, none of these assumptions is correct: quartet errors are positively correlated and occur with unknown probability, and the guide tree is often error prone. Here, we bring our work out of the purely theoretical setting. We present a variety of extensions which, while only slowing the algorithm down by a constant factor, make its performance nearly comparable to that of neighbour-joining, which requires O(n3) runtime. Our results suggest a new direction for quartet-based phylogenetic reconstruction that may yield striking speed improvements at minimal accuracy cost.
Towards a Practical O(n logn) Phylogeny Algorithm
14-25
true
https://link.springer.com/10.1007%2F978-3-642-23038-7_2
978-3-642-23037-0
978-3-642-23038-7
Algorithms in Bioinformatics
Brown
Daniel G.
University of Waterloo
David R. Cheriton School of Computer Science, University of Waterloo, N2L 3G1, Waterloo, ON, Canada
Truszkowski
Jakub
Springer Nature - SN SciGraph project
Berlin, Heidelberg
Springer Berlin Heidelberg
dimensions_id
pub.1050915819
Przytycka
Teresa M.
f28b5f8050ff284410c0f206111750227f527cd3e4e7278035d8befd7527eb4a
readcube_id
Statistics
Mathematical Sciences
10.1007/978-3-642-23038-7_2
doi