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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>
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Alignment
MUSCLE 
Curation
Gblocks
Phylogeny
PhyML
Tree Rendering
TreeDyn |
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Curation results
Figure 1: Selected alignment blocks (underlined in blue ).
Input:
Outputs:
Cured alignment in FASTA Format Cured alignment in PHYLIP FormatConserved positions: 46%
Taxon names association table
| Output Taxon Name | Original (Long) Taxon Name | |
|---|---|---|
| Aquifex_ae | Aquifex_aeolicus | (PHYLIP) |
| Aquifex_aeolicu | Aquifex_aeolicus | (HTML) |
| Aquifex_aeolicus | Aquifex_aeolicus | (FASTA, Guide tree) |
| Bacillus_C | Bacillus_Cereus_TAGGTATGGGGCAGCTATAATGCAAGTCGAGCGAATGGATTAAGAGCTTGCTCTTATGAAGTT | (PHYLIP) |
| Bacillus_Cereus | Bacillus_Cereus_TAGGTATGGGGCAGCTATAATGCAAGTCGAGCGAATGGATTAAGAGCTTGCTCTTATGAAGTT | (HTML) |
| Bacillus_Cereus_TAGGTATGGGGCAGCTATAATGCAAGTCGAGCGAATGGATTAAGAGCT | Bacillus_Cereus_TAGGTATGGGGCAGCTATAATGCAAGTCGAGCGAATGGATTAAGAGCTTGCTCTTATGAAGTT | (Guide tree) |
| Bacillus_Cereus_TAGGTATGGGGCAGCTATAATGCAAGTCGAGCGAATGGATTAAGAGCTTGCTCTTATGAAGTT | Bacillus_Cereus_TAGGTATGGGGCAGCTATAATGCAAGTCGAGCGAATGGATTAAGAGCTTGCTCTTATGAAGTT | (FASTA) |
| Bacillus_P | Bacillus_Paramycoides | (PHYLIP) |
| Bacillus_Paramy | Bacillus_Paramycoides | (HTML) |
| Bacillus_Paramycoides | Bacillus_Paramycoides | (FASTA, Guide tree) |
| Bacillus_s | Bacillus_sp_CTAATACATGCAAGTCGAGCGAACTGATTAGAAGCTTGCTTCTATGACGTTAGCGGCGGACGGGTGA | (PHYLIP) |
| Bacillus_sp_CTA | Bacillus_sp_CTAATACATGCAAGTCGAGCGAACTGATTAGAAGCTTGCTTCTATGACGTTAGCGGCGGACGGGTGA | (HTML) |
| Bacillus_sp_CTAATACATGCAAGTCGAGCGAACTGATTAGAAGCTTGCTTCTATGACGTTA | Bacillus_sp_CTAATACATGCAAGTCGAGCGAACTGATTAGAAGCTTGCTTCTATGACGTTAGCGGCGGACGGGTGA | (Guide tree) |
| Bacillus_sp_CTAATACATGCAAGTCGAGCGAACTGATTAGAAGCTTGCTTCTATGACGTTAGCGGCGGACGGGTGA | Bacillus_sp_CTAATACATGCAAGTCGAGCGAACTGATTAGAAGCTTGCTTCTATGACGTTAGCGGCGGACGGGTGA | (FASTA) |
| Cytobacill | Cytobacillus_Kochii_TGCAAGTCGAGCGAATCTGAGGGAGCTTGCTCCCAAAGATTAGCGGCGGACGGGTGAGT | (PHYLIP) |
| Cytobacillus_Ko | Cytobacillus_Kochii_TGCAAGTCGAGCGAATCTGAGGGAGCTTGCTCCCAAAGATTAGCGGCGGACGGGTGAGT | (HTML) |
| Cytobacillus_Kochii_TGCAAGTCGAGCGAATCTGAGGGAGCTTGCTCCCAAAGATTAGC | Cytobacillus_Kochii_TGCAAGTCGAGCGAATCTGAGGGAGCTTGCTCCCAAAGATTAGCGGCGGACGGGTGAGT | (Guide tree) |
| Cytobacillus_Kochii_TGCAAGTCGAGCGAATCTGAGGGAGCTTGCTCCCAAAGATTAGCGGCGGACGGGTGAGT | Cytobacillus_Kochii_TGCAAGTCGAGCGAATCTGAGGGAGCTTGCTCCCAAAGATTAGCGGCGGACGGGTGAGT | (FASTA) |
| Exiguobact | Exiguobacterium_Profundum_ATTAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCCTAATACATG | (PHYLIP) |
| Exiguobacterium | Exiguobacterium_Profundum_ATTAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCCTAATACATG | (HTML) |
| Exiguobacterium_Profundum_ATTAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGG | Exiguobacterium_Profundum_ATTAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCCTAATACATG | (Guide tree) |
| Exiguobacterium_Profundum_ATTAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCCTAATACATG | Exiguobacterium_Profundum_ATTAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGTGCCTAATACATG | (FASTA) |
| Laceyella | Laceyella_Sacchari_ATTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCATGCCTAATACATGCAAGTCG | (PHYLIP) |
| Laceyella_Sacch | Laceyella_Sacchari_ATTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCATGCCTAATACATGCAAGTCG | (HTML) |
| Laceyella_Sacchari_ATTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCATGCCT | Laceyella_Sacchari_ATTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCATGCCTAATACATGCAAGTCG | (Guide tree) |
| Laceyella_Sacchari_ATTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCATGCCTAATACATGCAAGTCG | Laceyella_Sacchari_ATTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCATGCCTAATACATGCAAGTCG | (FASTA) |
| Micromonos | Micromonospora_Chersina_GTACTCGAGCGGCGAACGGGTGAGTAACACGTGAGCAACCTGCCCTAGGCTTTGG | (PHYLIP) |
| Micromonospora | Micromonospora_Chersina_GTACTCGAGCGGCGAACGGGTGAGTAACACGTGAGCAACCTGCCCTAGGCTTTGG | (HTML) |
| Micromonospora_Chersina_GTACTCGAGCGGCGAACGGGTGAGTAACACGTGAGCAACC | Micromonospora_Chersina_GTACTCGAGCGGCGAACGGGTGAGTAACACGTGAGCAACCTGCCCTAGGCTTTGG | (Guide tree) |
| Micromonospora_Chersina_GTACTCGAGCGGCGAACGGGTGAGTAACACGTGAGCAACCTGCCCTAGGCTTTGG | Micromonospora_Chersina_GTACTCGAGCGGCGAACGGGTGAGTAACACGTGAGCAACCTGCCCTAGGCTTTGG | (FASTA) |
| Pseudoalte | Pseudoalteromonas_Maricaloris_TTAGTTGGGGGGGGGGGGGGGGGGGGGTTTTTTTTTAAGTATCGTTTTC | (PHYLIP) |
| Pseudoalteromon | Pseudoalteromonas_Maricaloris_TTAGTTGGGGGGGGGGGGGGGGGGGGGTTTTTTTTTAAGTATCGTTTTC | (HTML) |
| Pseudoalteromonas_Maricaloris_TTAGTTGGGGGGGGGGGGGGGGGGGGGTTTTTTT | Pseudoalteromonas_Maricaloris_TTAGTTGGGGGGGGGGGGGGGGGGGGGTTTTTTTTTAAGTATCGTTTTC | (Guide tree) |
| Pseudoalteromonas_Maricaloris_TTAGTTGGGGGGGGGGGGGGGGGGGGGTTTTTTTTTAAGTATCGTTTTC | Pseudoalteromonas_Maricaloris_TTAGTTGGGGGGGGGGGGGGGGGGGGGTTTTTTTTTAAGTATCGTTTTC | (FASTA) |
| Shewanella | Shewanella_Algae | (PHYLIP) |
| Shewanella_Alga | Shewanella_Algae | (HTML) |
| Shewanella_Algae | Shewanella_Algae | (Guide tree, FASTA) |
| Streptomyc | Streptomyces_sp_GATGAACCTCCTTCGGGAGGGGATTAGTGGCGAACGGGTGAGTAACACGTGGGCAATCTGCCC | (PHYLIP) |
| Streptomyces_sp | Streptomyces_sp_GATGAACCTCCTTCGGGAGGGGATTAGTGGCGAACGGGTGAGTAACACGTGGGCAATCTGCCC | (HTML) |
| Streptomyces_sp_GATGAACCTCCTTCGGGAGGGGATTAGTGGCGAACGGGTGAGTAACAC | Streptomyces_sp_GATGAACCTCCTTCGGGAGGGGATTAGTGGCGAACGGGTGAGTAACACGTGGGCAATCTGCCC | (Guide tree) |
| Streptomyces_sp_GATGAACCTCCTTCGGGAGGGGATTAGTGGCGAACGGGTGAGTAACACGTGGGCAATCTGCCC | Streptomyces_sp_GATGAACCTCCTTCGGGAGGGGATTAGTGGCGAACGGGTGAGTAACACGTGGGCAATCTGCCC | (FASTA) |
| Stutzerimo | Stutzerimonas_Stutzeri_CGGCAATGCGGAGCTACAATGCAGTCGAGCGCATGAGTGGAGCTTGTTCTCTGATT | (PHYLIP) |
| Stutzerimonas_S | Stutzerimonas_Stutzeri_CGGCAATGCGGAGCTACAATGCAGTCGAGCGCATGAGTGGAGCTTGTTCTCTGATT | (HTML) |
| Stutzerimonas_Stutzeri_CGGCAATGCGGAGCTACAATGCAGTCGAGCGCATGAGTGGA | Stutzerimonas_Stutzeri_CGGCAATGCGGAGCTACAATGCAGTCGAGCGCATGAGTGGAGCTTGTTCTCTGATT | (Guide tree) |
| Stutzerimonas_Stutzeri_CGGCAATGCGGAGCTACAATGCAGTCGAGCGCATGAGTGGAGCTTGTTCTCTGATT | Stutzerimonas_Stutzeri_CGGCAATGCGGAGCTACAATGCAGTCGAGCGCATGAGTGGAGCTTGTTCTCTGATT | (FASTA) |
| Tepidibact | Tepidibacter_Formicigenes_ATTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCCTAACACATG | (PHYLIP) |
| Tepidibacter_Fo | Tepidibacter_Formicigenes_ATTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCCTAACACATG | (HTML) |
| Tepidibacter_Formicigenes_ATTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGG | Tepidibacter_Formicigenes_ATTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCCTAACACATG | (Guide tree) |
| Tepidibacter_Formicigenes_ATTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCCTAACACATG | Tepidibacter_Formicigenes_ATTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCCTAACACATG | (FASTA) |
| Thermoacti | Thermoactinomyces_Vulgaris | (PHYLIP) |
| Thermoactinomyc | Thermoactinomyces_Vulgaris | (HTML) |
| Thermoactinomyces_Vulgaris | Thermoactinomyces_Vulgaris | (Guide tree, FASTA) |
| Vibrio_Har | Vibrio_Harveyi_AAGGATTTCTTATAATCTCCCACACCCCCCCCCCCCCCCCCCTTCTTCCTCCCCCTTTAAGATT | (PHYLIP) |
| Vibrio_Harveyi | Vibrio_Harveyi_AAGGATTTCTTATAATCTCCCACACCCCCCCCCCCCCCCCCCTTCTTCCTCCCCCTTTAAGATT | (HTML) |
| Vibrio_Harveyi_AAGGATTTCTTATAATCTCCCACACCCCCCCCCCCCCCCCCCTTCTTCC | Vibrio_Harveyi_AAGGATTTCTTATAATCTCCCACACCCCCCCCCCCCCCCCCCTTCTTCCTCCCCCTTTAAGATT | (Guide tree) |
| Vibrio_Harveyi_AAGGATTTCTTATAATCTCCCACACCCCCCCCCCCCCCCCCCTTCTTCCTCCCCCTTTAAGATT | Vibrio_Harveyi_AAGGATTTCTTATAATCTCCCACACCCCCCCCCCCCCCCCCCTTCTTCCTCCCCCTTTAAGATT | (FASTA) |
| Virgibacil | Virgibacillus_Salarius | (PHYLIP) |
| Virgibacillus_S | Virgibacillus_Salarius | (HTML) |
| Virgibacillus_Salarius | Virgibacillus_Salarius | (FASTA, Guide tree) |
Download taxon names association tableMultiple sequence alignment editor:
(If you expect to edit the alignment by yourself, you can consult Jalview multiple alignment editor documentation
.)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)
