PhyML 3.1/3.0 aLRT (doc + aLRT)
Process Info:
Number of taxa: 34
Average sequences length: 279
(between 279 and 279)
Assumed to be: DNA
Computation:
Phylogeny: 18 seconds
Overall time: 18 seconds
Number of taxa: 34
Average sequences length: 279
(between 279 and 279)
Assumed to be: DNA
Computation:
Phylogeny: 18 seconds
Overall time: 18 seconds
The analysis was performed on the Phylogeny.fr platform and comprised the following steps. |
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Phylogeny
PhyML  + aLRT
Outputs: Settings: Model: HKY85 Statistical test: alrt Number of categories: 4 Gamma: estimated Invariable sites: estimated Remove gaps: enabled |
The phylogenetic tree was reconstructed using the maximum likelihood method implemented in the PhyML program (v3.1/3.0 aLRT). The HKY85 substitution model was selected assuming an estimated proportion of invariant sites (of 0.123) and 4 gamma-distributed rate categories to account for rate heterogeneity across sites. The gamma shape parameter was estimated directly from the data (gamma=2.278). Reliability for internal branch was assessed using the aLRT test (SH-Like). |
Please cite:
- Dereeper A., Audic S., Claverie J.M., Blanc G. BLAST-EXPLORER helps you building datasets for phylogenetic analysis. BMC Evol Biol. 2010 Jan 12;10:8. (PubMed)
- Dereeper A.*, Guignon V.*, Blanc G., Audic S., Buffet S., Chevenet F., Dufayard J.F., Guindon S., Lefort V., Lescot M., Claverie J.M., Gascuel O. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W465-9. Epub 2008 Apr 19. (PubMed) *: joint first authors
- Guindon S., Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003, Oct;52(5):696-704. (PubMed)
- Anisimova M., Gascuel O. Approximate likelihood ratio test for branchs: A fast, accurate and powerful alternative. Syst Biol. 2006, Aug;55(4):539-52. (PubMed)
