A new version of phylogeny.fr is available: https://v2.phylogeny.fr/!
Feel free to try it and give us feedbacks ! This is still a beta version and all comments will help us to improve it.
Send your comments to : Phylogeny.fr <phylogeny@igs.cnrs-mrs.fr>
Feel free to try it and give us feedbacks ! This is still a beta version and all comments will help us to improve it.
Send your comments to : Phylogeny.fr <phylogeny@igs.cnrs-mrs.fr>
| "One Click" Mode |
Alignment
MUSCLE 
Curation
Gblocks
Phylogeny
PhyML
Tree Rendering
TreeDyn |
Help  |
Phylogeny results
Figure 1: Phylogenetic tree.
Input:
Outputs:
Tree in Newick format (automatically recognized by MEGA if installed) Statistics fileSubstitution model: HKY85
Gamma shape parameter: 0.541
Transition/transversion ratio: 2.663
Number of categories: 4
Proportion of invariant: 0.000
Taxon names association table
| Output Taxon Name | Original (Long) Taxon Name | |
|---|---|---|
| Aquifex_aeolicus | Aquifex_aeolicus | (Newick) |
| Bacillus_Cereus_TAGGTATGGGGCAGCTATAATGCAAGTCGAGCGAATGGATTAAGAGCT | Bacillus_Cereus_TAGGTATGGGGCAGCTATAATGCAAGTCGAGCGAATGGATTAAGAGCTTGCTCTTATGAAGTT | (Newick) |
| Bacillus_Paramycoides | Bacillus_Paramycoides | (Newick) |
| Bacillus_sp_CTAATACATGCAAGTCGAGCGAACTGATTAGAAGCTTGCTTCTATGACGTTA | Bacillus_sp_CTAATACATGCAAGTCGAGCGAACTGATTAGAAGCTTGCTTCTATGACGTTAGCGGCGGACGGGTGA | (Newick) |
| Cytobacillus_Kochii_TGCAAGTCGAGCGAATCTGAGGGAGCTTGCTCCCAAAGATTAGC | Cytobacillus_Kochii_TGCAAGTCGAGCGAATCTGAGGGAGCTTGCTCCCAAAGATTAGCGGCGGACGGGTGAGT | (Newick) |
| Exiguobacterium_Profundum_ATTAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGG | Exiguobacterium_Profundum_ATTAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCCTAATACATG | (Newick) |
| Laceyella_Sacchari_ATTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCATGCCT | Laceyella_Sacchari_ATTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCATGCCTAATACATGCAAGTCG | (Newick) |
| Micromonospora_Chersina_GTACTCGAGCGGCGAACGGGTGAGTAACACGTGAGCAACC | Micromonospora_Chersina_GTACTCGAGCGGCGAACGGGTGAGTAACACGTGAGCAACCTGCCCTAGGCTTTGG | (Newick) |
| Pseudoalteromonas_Maricaloris_TTAGTTGGGGGGGGGGGGGGGGGGGGGTTTTTTT | Pseudoalteromonas_Maricaloris_TTAGTTGGGGGGGGGGGGGGGGGGGGGTTTTTTTTTAAGTATCGTTTTC | (Newick) |
| Shewanella_Algae | Shewanella_Algae | (Newick) |
| Streptomyces_sp_GATGAACCTCCTTCGGGAGGGGATTAGTGGCGAACGGGTGAGTAACAC | Streptomyces_sp_GATGAACCTCCTTCGGGAGGGGATTAGTGGCGAACGGGTGAGTAACACGTGGGCAATCTGCCC | (Newick) |
| Stutzerimonas_Stutzeri_CGGCAATGCGGAGCTACAATGCAGTCGAGCGCATGAGTGGA | Stutzerimonas_Stutzeri_CGGCAATGCGGAGCTACAATGCAGTCGAGCGCATGAGTGGAGCTTGTTCTCTGATT | (Newick) |
| Tepidibacter_Formicigenes_ATTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGG | Tepidibacter_Formicigenes_ATTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCCTAACACATG | (Newick) |
| Thermoactinomyces_Vulgaris | Thermoactinomyces_Vulgaris | (Newick) |
| Vibrio_Harveyi_AAGGATTTCTTATAATCTCCCACACCCCCCCCCCCCCCCCCCTTCTTCC | Vibrio_Harveyi_AAGGATTTCTTATAATCTCCCACACCCCCCCCCCCCCCCCCCTTCTTCCTCCCCCTTTAAGATT | (Newick) |
| Virgibacillus_Salarius | Virgibacillus_Salarius | (Newick) |
Download taxon names association tableTree viewer:
(requires Java 1.6 or above)
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)
