# A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood

**Olivier Gascuel**

CiteWeb id: 20030000014

CiteWeb score: 12076

DOI: 10.1080/10635150390235520

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 maximumlikelihood 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 fromplant 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/.

**A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood**" is placed in the Top 1000 of the best publications in CiteWeb. Also in the category Biology it is included to the Top 100. Additionally, the publicaiton "

**A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood**" is placed in the Top 100 among other scientific works published in 2003.

- www.jstor.org/stable/info/3651071
- hal-lirmm.ccsd.cnrs.fr/lirmm-00191949/document
- sysbio.oxfordjournals.org/content/52/5/696.full.pdf
- https://www.lirmm.fr/content/download/6364/119885/file/GG-SB-03.pdf
- www.ncbi.nlm.nih.gov/pubmed/14530136
- sysbio.oxfordjournals.org/content/52/5/696.short
- hal-lirmm.ccsd.cnrs.fr/lirmm-00191949v1
- ci.nii.ac.jp/naid/30016572343

Olivier Gascuel,

A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood(2003)## HTML code:

## Wiki code: