The analysis was performed on the Phylogeny.fr platform and comprised the following steps.
Alignment
MUSCLE
Outputs:
Settings: Run mode:full processing mode
Sequences were aligned with MUSCLE (v3.8.31) configured for highest accuracy (MUSCLE with default settings).
Curation
Gblocks
Outputs:
Settings: Min. seq. for flank pos.:85% Max. contig. nonconserved pos.:8 Min. block length:10 Gaps in final blocks:no
After alignment, ambiguous regions (i.e. containing gaps and/or poorly aligned) were removed with Gblocks (v0.91b) using the following parameters:
-minimum length of a block after gap cleaning: 10
-no gap positions were allowed in the final alignment
-all segments with contiguous nonconserved positions bigger than 8 were rejected
-minimum number of sequences for a flank position: 85%
Settings: Model:WAG 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 WAG substitution model was selected assuming an estimated proportion of invariant sites (of 0.000) and 4 gamma-distributed rate categories to account for rate heterogeneity across sites. The gamma shape parameter was estimated directly from the data (gamma=0.845). Reliability for internal branch was assessed using the aLRT test (SH-Like).
Tree Rendering
TreeDyn
Outputs:
Settings: Conformation:rectangular Legend:displayed Branch annotation:bootstrap Font:Times 8 normal
Graphical representation and edition of the phylogenetic tree were performed with TreeDyn (v198.3).
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
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, Mar 19;32(5):1792-7. (PubMed)
Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000, Apr;17(4):540-52. (PubMed)
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)
Chevenet F., Brun C., Banuls AL., Jacq B., Chisten R. TreeDyn: towards dynamic graphics and annotations for analyses of trees. BMC Bioinformatics. 2006, Oct 10;7:439. (PubMed)