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: WAG
Gamma shape parameter: 0.867
Number of categories: 4
Proportion of invariant: 0.112
Taxon names association table
| Output Taxon Name | Original (Long) Taxon Name | |
|---|---|---|
| sp_P00044_CYC1_YEAST_Cytochrome_c_isoform_1_OS=Saccharomyces_cer | sp|P00044|CYC1_YEAST_Cytochrome_c_isoform_1_OS=Saccharomyces_cerevisiae_(strain | (Newick) |
| sp_P00045_CYC7_YEAST_Cytochrome_c_isoform_2_OS=Saccharomyces_cer | sp|P00045|CYC7_YEAST_Cytochrome_c_isoform_2_OS=Saccharomyces_cerevisiae_(strain | (Newick) |
| sp_P04657_CYC1_DROME_Cytochrome_c-1_OS=Drosophila_melanogaster_O | sp|P04657|CYC1_DROME_Cytochrome_c-1_OS=Drosophila_melanogaster_OX=7227_GN=Cyt-c | (Newick) |
| sp_P19974_CYC21_CAEEL_Cytochrome_c_2.1_OS=Caenorhabditis_elegans | sp|P19974|CYC21_CAEEL_Cytochrome_c_2.1_OS=Caenorhabditis_elegans_OX=6239_GN=cyc | (Newick) |
| sp_P62897_CYC_MOUSE_Cytochrome_c_somatic_OS=Mus_musculus_OX=1009 | sp|P62897|CYC_MOUSE_Cytochrome_c,_somatic_OS=Mus_musculus_OX=10090_GN=Cycs_PE=1 | (Newick) |
| sp_P62898_CYC_RAT_Cytochrome_c_somatic_OS=Rattus_norvegicus_OX=1 | sp|P62898|CYC_RAT_Cytochrome_c,_somatic_OS=Rattus_norvegicus_OX=10116_GN=Cycs_P | (Newick) |
| sp_P84029_CYC2_DROME_Cytochrome_c-2_OS=Drosophila_melanogaster_O | sp|P84029|CYC2_DROME_Cytochrome_c-2_OS=Drosophila_melanogaster_OX=7227_GN=Cyt-c | (Newick) |
| sp_P99999_CYC_HUMAN_Cytochrome_c_OS=Homo_sapiens_OX=9606_GN=CYCS | sp|P99999|CYC_HUMAN_Cytochrome_c_OS=Homo_sapiens_OX=9606_GN=CYCS_PE=1_SV=2 | (Newick) |
| sp_Q23240_CYC22_CAEEL_Probable_cytochrome_c_2.2_OS=Caenorhabditi | sp|Q23240|CYC22_CAEEL_Probable_cytochrome_c_2.2_OS=Caenorhabditis_elegans_OX=62 | (Newick) |
| sp_Q640U4_CYC1_XENTR_Cytochrome_c_somatic_OS=Xenopus_tropicalis | sp|Q640U4|CYC1_XENTR_Cytochrome_c,_somatic_OS=Xenopus_tropicalis_OX=8364_GN=cyc | (Newick) |
| sp_Q6DKE1_CYC2_XENLA_Cytochrome_c_testis-specific_OS=Xenopus_lae | sp|Q6DKE1|CYC2_XENLA_Cytochrome_c,_testis-specific_OS=Xenopus_laevis_OX=8355_GN | (Newick) |
| sp_Q6IQM2_CYC_DANRE_Cytochrome_c_OS=Danio_rerio_OX=7955_GN=cyc_P | sp|Q6IQM2|CYC_DANRE_Cytochrome_c_OS=Danio_rerio_OX=7955_GN=cyc_PE=3_SV=3 | (Newick) |
| sp_Q6PBF4_CYC2_XENTR_Cytochrome_c_testis-specific_OS=Xenopus_tro | sp|Q6PBF4|CYC2_XENTR_Cytochrome_c,_testis-specific_OS=Xenopus_tropicalis_OX=836 | (Newick) |
| tr_A0A1L8FW52_A0A1L8FW52_XENLA_Cytochrome_c_testis-specific_OS=X | tr|A0A1L8FW52|A0A1L8FW52_XENLA_Cytochrome_c,_testis-specific_OS=Xenopus_laevis | (Newick) |
| tr_D4A5L9_D4A5L9_RAT_Cytochrome_c_somatic_like_2_OS=Rattus_norve | tr|D4A5L9|D4A5L9_RAT_Cytochrome_c,_somatic_like_2_OS=Rattus_norvegicus_OX=10116 | (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)
