local support

[Andrea]

Hello,

I performed a multi-locus analysis on SATé, using Fast Tree estimator. The result was a tree with node values ranging from 0.4 to 1 (to visualised I had used FigTree). Please tell me, which is the interpretation of these values? Their interpretation can be similar than Posterior Probability values on Bayesian Inference?

Thanks in advance,

[Jamie Oaks]

Hi,

These values are "SH-like" local support values:

http://www.microbesonline.org/fasttree/#Support

Basically, FastTree does a very fast assessment of the support for each

split in the estimated ML tree by performing an SH-test on the three

nearest-neighbor topologies of each split.  This is also done in PhyML,

and is discussed in section 1.6 of this paper:

    Guindon, S., Delsuc, F., Dufayard, J.-F., & Gascuel, O. (2009).

    Estimating maximum likelihood phylogenies with PhyML. Methods in

    molecular biology (Clifton, N.J.), 537, 113–137.

    doi:10.1007/978-1-59745-251-9_6

And here is the paper describing the SH-test:

    Shimodaira, H., & Hasegawa, M. (1999). Multiple comparisons of

    log-likelihoods with applications to phylogenetic inference.

    Molecular Biololgy and Evolution, 16, 1114–1116.

These values are calculated by FastTree on a fixed alignment (i.e., the

alignment of a given iteration of of SATe) and thus do not capture any

uncertainty in the alignment. In other words, these values are not

summarizing any variation in the trees among iterations of the SATe

algorithm.

Like bootstrap support values (and unlike Bayesian posterior

probabilities), they are non-parametric.

I hope this helps,

Jamie

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[Andrea Acurio]

You helped me a lot. Thanks!

2012/9/13 Jamie Oaks <joa...@gmail.com>