"One Click" Mode
Alignment
MUSCLE
->
Curation
Gblocks
->
Phylogeny
PhyML
->
Tree Rendering
TreeDyn
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Process Info:
Number of taxa: 15
Average sequences length: 1264
   (between 1241 and 1353)

Assumed to be: protein

Computation:
Alignment: 2 seconds
Curation: 3 seconds
Phylogeny: 154 seconds
Tree Rendering: 2 seconds

Overall time: 161 seconds
User Inputs
Input
The analysis was performed on the Phylogeny.fr platform and comprised the following steps.
↓
 
Alignment
MUSCLE doc

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 doc

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%
↓
 
Phylogeny
PhyML doc + aLRT

Outputs:


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 doc

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:
  1. 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)
  2. 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
  3. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, Mar 19;32(5):1792-7. (PubMed)
  4. 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)
  5. 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)
  6. 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)
  7. 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)

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