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Approximate Likelihood-Ratio Test for Branches: A Fast, Accurate, and Powerful Alternative

Equipe Méthodes et Algorithmes pour la Bioinformatique LIRMM-CNRS, Université Montpellier II, Montpellier 34392, France.
Systematic Biology (Impact Factor: 11.53). 09/2006; 55(4):539-52. DOI: 10.1080/10635150600755453
Source: PubMed

ABSTRACT We revisit statistical tests for branches of evolutionary trees reconstructed upon molecular data. A new, fast, approximate likelihood-ratio test (aLRT) for branches is presented here as a competitive alternative to nonparametric bootstrap and Bayesian estimation of branch support. The aLRT is based on the idea of the conventional LRT, with the null hypothesis corresponding to the assumption that the inferred branch has length 0. We show that the LRT statistic is asymptotically distributed as a maximum of three random variables drawn from the chi(0)2 + chi(1)2 distribution. The new aLRT of interior branch uses this distribution for significance testing, but the test statistic is approximated in a slightly conservative but practical way as 2(l1- l2), i.e., double the difference between the maximum log-likelihood values corresponding to the best tree and the second best topological arrangement around the branch of interest. Such a test is fast because the log-likelihood value l2 is computed by optimizing only over the branch of interest and the four adjacent branches, whereas other parameters are fixed at their optimal values corresponding to the best ML tree. The performance of the new test was studied on simulated 4-, 12-, and 100-taxon data sets with sequences of different lengths. The aLRT is shown to be accurate, powerful, and robust to certain violations of model assumptions. The aLRT is implemented within the algorithm used by the recent fast maximum likelihood tree estimation program PHYML (Guindon and Gascuel, 2003).

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    • "After alignment, regions with gaps were removed and 2354 gap-free sites were used in maximum likelihood (ML) phylogenetic analysis as implemented in PhyML (v3.0 aLRT) (Anisimova and Gascuel, 2006; Guindon and Gascuel, 2003). The reliability for the internal branches was assessed using the approximate likelihood ratio test (aLRT – SH-Like) (Anisimova and Gascuel, 2006). Graphical representation and editing of the phylogenetic trees were performed with TreeDyn (v 198.3) (Chevenet et al., 2006). "
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    • "only CDS and CDS + tRNA, were prepared using a in-house Perl script to carry out the phylogenetic analysis. All the sequences were aligned using MUSCLE (Edgar, 2004) and the phylogenetic tree was constructed using the PhyML (Anisimova and Gascuel, 2006) option in Sea-View software (Gouy et al., 2010), with the following parameters: Model = GTR, Branch support = aLRT (SH like) and the tree searching operation = best of NNI and SPR. Further, refinement of the phylogenetic tree was done using FigTree (Morariu et al., 2009). "
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    • "only CDS and CDS + tRNA, were prepared using a in-house Perl script to carry out the phylogenetic analysis. All the sequences were aligned using MUSCLE (Edgar, 2004) and the phylogenetic tree was constructed using the PhyML (Anisimova and Gascuel, 2006) option in Sea-View software (Gouy et al., 2010), with the following parameters: Model = GTR, Branch support = aLRT (SH like) and the tree searching operation = best of NNI and SPR. Further, refinement of the phylogenetic tree was done using FigTree (Morariu et al., 2009). "
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