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

@article{Guindon2003ASF, title={A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.}, author={St{\'e}phane Guindon and Olivier Gascuel}, journal={Systematic biology}, year={2003}, volume={52 5}, pages={ 696-704 } }

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 methodâ€¦Â

## 15,948 Citations

### RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees

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This paper presents the latest release of the program RAxML-III for rapid maximum likelihood-based inference of large evolutionary trees which allows for computation of 1.000-taxon trees in less than 24 hours on a single PC processor.

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A novel, partially randomized algorithm and new parsimony-based rearrangement heuristics are implemented in a sequential and parallel program called RAxML, which shows run time improvements > 25% over parallel fastDNAml yielding exactly the same results.

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Improvements to FastTree are described that improve its accuracy without sacrificing scalability, and FastTree 2 allows the inference of maximum-likelihood phylogenies for huge alignments.

### IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

- Biology, Computer ScienceMolecular biology and evolution
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It is shown that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented and found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space.

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- BiologySystematic biology
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### RAxML and FastTree: Comparing Two Methods for Large-Scale Maximum Likelihood Phylogeny Estimation

- Computer SciencePloS one
- 2011

This study shows that very large phylogenies can be estimated very quickly using FastTree, with little (and in some cases no) degradation in tree accuracy, as compared to RAxML.

### An efficient program for phylogenetic inference using simulated annealing

- Biology19th IEEE International Parallel and Distributed Processing Symposium
- 2005

A new program RAxML-SA (Randomized Axelerated Maximum Likelihood with Simulated-Annealing) is presented that combines simulated annealing and hill-climbing techniques to improve the quality of final trees.

### On a New Quartet-Based Phylogeny Reconstruction Algorithm

- MathematicsBIOCOMP
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It is common that certain incorrect trees can have likelihood values at least as large as that of the correct tree, suggesting that even if the authors are able to find a truly globally optimal tree under the maximum likelihood criterion, this tree may not necessarily be the correct phylogenetic tree.

### Estimating phylogenies under maximum likelihood : A very large-scale neighborhood approach

- Computer Science
- 2008

This work adapts Very Large-Scale Neighborhood techniques to estimate phylogenies of large datasets of nucleotide sequences under the maximum likelihood criterion, and shows that the use of the VLSN techniques speeds up convergence to topological local optima, and increases the overall performances of stochastic-based search algorithms.

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