Phylogeny.fr: "One Click" Mode

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"One Click" Mode

Alignment
MUSCLE

Curation
Gblocks

Phylogeny
PhyML

Tree Rendering
TreeDyn

Help

Alignment results

Figure 1: Sequence alignment.
Legend:
Similar residues are colored as the most conserved one (according to BLOSUM62).
Average BLOSUM62 score: Max: 3.0 Mid: 1.5 Low: 0.5

Input:

Sequences

Outputs:

Alignment in Fasta format

Alignment in Phylip format

Alignment in Clustal format

Taxon names association table

Table I: Taxon names association table
Output Taxon Name	Original (Long) Taxon Name

A5FNY2.1:4-171_RecName:_Full=Shikimate_kinase;_Short=SK_[Flavobacterium_johnson	A5FNY2.1:4-171_RecName:_Full=Shikimate_kinase;_Short=SK_[Flavobacterium_johnson	(FASTA)
A5FNY2.1_4	A5FNY2.1:4-171_RecName:_Full=Shikimate_kinase;_Short=SK_[Flavobacterium_johnson	(PHYLIP, HTML, Clustal)
A5FNY2.1_4-171_RecName_Full=Shikimate_kinase_Short=SK_Flavobacte	A5FNY2.1:4-171_RecName:_Full=Shikimate_kinase;_Short=SK_[Flavobacterium_johnson	(Guide tree)
A6GZJ6.1:4-171_RecName:_Full=Shikimate_kinase;_Short=SK_[Flavobacterium_psychro	A6GZJ6.1:4-171_RecName:_Full=Shikimate_kinase;_Short=SK_[Flavobacterium_psychro	(FASTA)
A6GZJ6.1_4	A6GZJ6.1:4-171_RecName:_Full=Shikimate_kinase;_Short=SK_[Flavobacterium_psychro	(HTML, PHYLIP, Clustal)
A6GZJ6.1_4-171_RecName_Full=Shikimate_kinase_Short=SK_Flavobacte	A6GZJ6.1:4-171_RecName:_Full=Shikimate_kinase;_Short=SK_[Flavobacterium_psychro	(Guide tree)
A6L011.1:2-175_RecName:_Full=Shikimate_kinase;_Short=SK_[Phocaeicola_vulgatus_A	A6L011.1:2-175_RecName:_Full=Shikimate_kinase;_Short=SK_[Phocaeicola_vulgatus_A	(FASTA)
A6L011.1_2	A6L011.1:2-175_RecName:_Full=Shikimate_kinase;_Short=SK_[Phocaeicola_vulgatus_A	(HTML, PHYLIP, Clustal)
A6L011.1_2-175_RecName_Full=Shikimate_kinase_Short=SK_Phocaeicol	A6L011.1:2-175_RecName:_Full=Shikimate_kinase;_Short=SK_[Phocaeicola_vulgatus_A	(Guide tree)
A6LFQ8.1:4-173_RecName:_Full=Shikimate_kinase;_Short=SK_[Parabacteroides_distas	A6LFQ8.1:4-173_RecName:_Full=Shikimate_kinase;_Short=SK_[Parabacteroides_distas	(FASTA)
A6LFQ8.1_4	A6LFQ8.1:4-173_RecName:_Full=Shikimate_kinase;_Short=SK_[Parabacteroides_distas	(Clustal, HTML, PHYLIP)
A6LFQ8.1_4-173_RecName_Full=Shikimate_kinase_Short=SK_Parabacter	A6LFQ8.1:4-173_RecName:_Full=Shikimate_kinase;_Short=SK_[Parabacteroides_distas	(Guide tree)
Q8A2B2.1:4-155_RecName:_Full=Shikimate_kinase;_Short=SK_[Bacteroides_thetaiotao	Q8A2B2.1:4-155_RecName:_Full=Shikimate_kinase;_Short=SK_[Bacteroides_thetaiotao	(FASTA)
Q8A2B2.1_4	Q8A2B2.1:4-155_RecName:_Full=Shikimate_kinase;_Short=SK_[Bacteroides_thetaiotao	(Clustal, HTML, PHYLIP)
Q8A2B2.1_4-155_RecName_Full=Shikimate_kinase_Short=SK_Bacteroide	Q8A2B2.1:4-155_RecName:_Full=Shikimate_kinase;_Short=SK_[Bacteroides_thetaiotao	(Guide tree)

Download taxon names association table

Multiple sequence alignment editor:

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(If you expect to edit the alignment by yourself, you can consult Jalview multiple alignment editor documentation doc

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)

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