|
Hot
Paper in Environment/Ecology
|
|
"A simple, fast, and accurate
algorithm to estimate large phylogenies by maximum likelihood,"
by Stephane Guindon and Olivier Gascuel, Systematic Biology, 52(2):
696-704, October 2003.
Authors' affiliations: LIRMM, CNRS,
Montpellier, France; University of Auckland, New Zealand]
Abstract:
"The increase in the number of large data sets and the complexity of
current probabilistic sequence evolution models necessitates fast and reliable
phylogeny reconstruction methods. We describe a new approach, based on the
maximum-likelihood principle, which clearly satisfies these requirements. The
core of this method is a simple hill-climbing algorithm that adjusts tree
topology and branch lengths simultaneously. This algorithm starts from an
initial tree built by a fast distance-based method and modifies this tree to
improve its likelihood at each iteration. Due to this simultaneous adjustment
of the topology and branch lengths, only a few iterations are sufficient to
reach an optimum. We used extensive and realistic computer simulations to show
that the topological accuracy of this new method is at least as high as that
of the existing maximum-likelihood programs and much higher than the
performance of distance-based and parsimony approaches. The reduction of
computing time is dramatic in comparison with other maximum-likelihood
packages, while the likelihood maximization ability tends to be higher. For
example, only 12 min were required on a standard personal computer to analyze
a data set consisting of 500 rbcL sequences with 1,428 base pairs from plant
plastids, thus reaching a speed of the same order as some popular
distance-based and parsimony algorithms. This new method is implemented in the
PHYML program, which is freely available on our web page: http://www.lirmm.fr/w3ifa/MAAS/."
This 2003 report from Systematic Biology
was cited 29 times in current journal articles indexed by Thomson Scientific
during May-June 2005. No other paper published since 2003 and categorized by
Thomson under the heading of environment/ecology attracted a higher number of
citations during that two-month period. Prior to the most recent bimonthly
count, citations to the paper have accrued as follows:
March-April 2005: 19 citations
January-February 2005: 17
November-December 2004: 4
September-October 2004: 11
July-August 2004: 4
May-June 2004: 4
March-April 2004: 1
January-February 2004: 1
Total citations to date: 90
SOURCE: Hot
Papers Database (Included with a subscription to the ISI print newsletter Science
Watch®, available from the ISI
Research Services Group. Packaged on a CD-ROM that is mailed with each Science
Watch issue, the Hot
Papers Database contains data on hundreds of highly cited papers published
during the last two years. User interface permits searching by author,
organization, journal, field, and more. Total citations, as well as citations
accrued during successive bimonthly periods, can be assessed and graphed. An
updated CD containing the most recent bimonthly data is mailed with every new
issue of Science
Watch,
six times a year. The CD also includes an electronic version of the Science
Watch
issue in HTML format, for personal desktop access.)
|
cites
:
View the past and present 
