Phylogeny.fr: "One Click" Mode

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"One Click" Mode

Alignment
MUSCLE

Curation
Gblocks

Phylogeny
PhyML

Tree Rendering
TreeDyn

Help

Phylogeny results

Figure 1: Phylogenetic tree.

Input:

Alignment

Outputs:

Tree in Newick format (automatically recognized by MEGA if installed)

Statistics file
Substitution model: HKY85
Gamma shape parameter: 0.664
Transition/transversion ratio: 7.325
Number of categories: 4
Proportion of invariant: 0.000

Taxon names association table

Download taxon names association table

Tree 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)

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Output Taxon Name	Original (Long) Taxon Name

CP035739.1_2909349-2909537_Pseudomonas_aeruginosa_strain_1334/14	CP035739.1:2909349-2909537_Pseudomonas_aeruginosa_strain_1334/14_chromosome,_co	(Newick)
CP035739.1_2951993-2953352_Pseudomonas_aeruginosa_strain_1334/14	CP035739.1:2951993-2953352_Pseudomonas_aeruginosa_strain_1334/14_chromosome,_co	(Newick)
CP035739.1_2952715-2952771_Pseudomonas_aeruginosa_strain_1334/14	CP035739.1:2952715-2952771_Pseudomonas_aeruginosa_strain_1334/14_chromosome,_co	(Newick)
CP035739.1_2953855-2953973_Pseudomonas_aeruginosa_strain_1334/14	CP035739.1:2953855-2953973_Pseudomonas_aeruginosa_strain_1334/14_chromosome,_co	(Newick)
CP035739.1_5669617-5669783_Pseudomonas_aeruginosa_strain_1334/14	CP035739.1:5669617-5669783_Pseudomonas_aeruginosa_strain_1334/14_chromosome,_co	(Newick)
CP035739.1_5669730-5669783_Pseudomonas_aeruginosa_strain_1334/14	CP035739.1:5669730-5669783_Pseudomonas_aeruginosa_strain_1334/14_chromosome,_co	(Newick)
CP035739.1_5674140-5674333_Pseudomonas_aeruginosa_strain_1334/14	CP035739.1:5674140-5674333_Pseudomonas_aeruginosa_strain_1334/14_chromosome,_co	(Newick)
CP195318.1_4991275-4992634_Pseudomonas_aeruginosa_strain_549457	CP195318.1:4991275-4992634_Pseudomonas_aeruginosa_strain_549457_chromosome_1,_c	(Newick)
CP195318.1_4991997-4992053_Pseudomonas_aeruginosa_strain_549457	CP195318.1:4991997-4992053_Pseudomonas_aeruginosa_strain_549457_chromosome_1,_c	(Newick)
CP195318.1_4993137-4993255_Pseudomonas_aeruginosa_strain_549457	CP195318.1:4993137-4993255_Pseudomonas_aeruginosa_strain_549457_chromosome_1,_c	(Newick)
CP195318.1_5833936-5834124_Pseudomonas_aeruginosa_strain_549457	CP195318.1:5833936-5834124_Pseudomonas_aeruginosa_strain_549457_chromosome_1,_c	(Newick)
CP195320.1_2696462-2697821_Pseudomonas_aeruginosa_strain_154012	CP195320.1:2696462-2697821_Pseudomonas_aeruginosa_strain_154012_chromosome_1,_c	(Newick)
CP195320.1_2697184-2697240_Pseudomonas_aeruginosa_strain_154012	CP195320.1:2697184-2697240_Pseudomonas_aeruginosa_strain_154012_chromosome_1,_c	(Newick)
CP195320.1_2698324-2698442_Pseudomonas_aeruginosa_strain_154012	CP195320.1:2698324-2698442_Pseudomonas_aeruginosa_strain_154012_chromosome_1,_c	(Newick)
CP195320.1_357183-357374_Pseudomonas_aeruginosa_strain_154012_ch	CP195320.1:357183-357374_Pseudomonas_aeruginosa_strain_154012_chromosome_1,_com	(Newick)
CP195320.1_6146197-6146388_Pseudomonas_aeruginosa_strain_154012	CP195320.1:6146197-6146388_Pseudomonas_aeruginosa_strain_154012_chromosome_1,_c	(Newick)
CP195321.1_1047493-1047684_Pseudomonas_aeruginosa_strain_130364	CP195321.1:1047493-1047684_Pseudomonas_aeruginosa_strain_130364_chromosome_1,_c	(Newick)
CP195321.1_3416939-3418298_Pseudomonas_aeruginosa_strain_130364	CP195321.1:3416939-3418298_Pseudomonas_aeruginosa_strain_130364_chromosome_1,_c	(Newick)
CP195321.1_3417661-3417717_Pseudomonas_aeruginosa_strain_130364	CP195321.1:3417661-3417717_Pseudomonas_aeruginosa_strain_130364_chromosome_1,_c	(Newick)
CP195321.1_3418801-3418919_Pseudomonas_aeruginosa_strain_130364	CP195321.1:3418801-3418919_Pseudomonas_aeruginosa_strain_130364_chromosome_1,_c	(Newick)
CP195321.1_459723-459914_Pseudomonas_aeruginosa_strain_130364_ch	CP195321.1:459723-459914_Pseudomonas_aeruginosa_strain_130364_chromosome_1,_com	(Newick)
CP195321.1_830185-830303_Pseudomonas_aeruginosa_strain_130364_ch	CP195321.1:830185-830303_Pseudomonas_aeruginosa_strain_130364_chromosome_1,_com	(Newick)
CP195321.1_830806-832165_Pseudomonas_aeruginosa_strain_130364_ch	CP195321.1:830806-832165_Pseudomonas_aeruginosa_strain_130364_chromosome_1,_com	(Newick)
CP195321.1_831387-831443_Pseudomonas_aeruginosa_strain_130364_ch	CP195321.1:831387-831443_Pseudomonas_aeruginosa_strain_130364_chromosome_1,_com	(Newick)
CP195322.1_3656784-3656975_Pseudomonas_aeruginosa_strain_130275	CP195322.1:3656784-3656975_Pseudomonas_aeruginosa_strain_130275_chromosome_1,_c	(Newick)
CP195322.1_4366248-4366439_Pseudomonas_aeruginosa_strain_130275	CP195322.1:4366248-4366439_Pseudomonas_aeruginosa_strain_130275_chromosome_1,_c	(Newick)
CP195322.1_5786540-5786658_Pseudomonas_aeruginosa_strain_130275	CP195322.1:5786540-5786658_Pseudomonas_aeruginosa_strain_130275_chromosome_1,_c	(Newick)
CP195322.1_5787161-5788520_Pseudomonas_aeruginosa_strain_130275	CP195322.1:5787161-5788520_Pseudomonas_aeruginosa_strain_130275_chromosome_1,_c	(Newick)
CP195322.1_5787742-5787798_Pseudomonas_aeruginosa_strain_130275	CP195322.1:5787742-5787798_Pseudomonas_aeruginosa_strain_130275_chromosome_1,_c	(Newick)
CP195323.1_126436-127795_Pseudomonas_aeruginosa_strain_129980_ch	CP195323.1:126436-127795_Pseudomonas_aeruginosa_strain_129980_chromosome_1,_com	(Newick)
CP195323.1_127158-127214_Pseudomonas_aeruginosa_strain_129980_ch	CP195323.1:127158-127214_Pseudomonas_aeruginosa_strain_129980_chromosome_1,_com	(Newick)
CP195323.1_128298-128416_Pseudomonas_aeruginosa_strain_129980_ch	CP195323.1:128298-128416_Pseudomonas_aeruginosa_strain_129980_chromosome_1,_com	(Newick)
CP195323.1_5983419-5983610_Pseudomonas_aeruginosa_strain_129980	CP195323.1:5983419-5983610_Pseudomonas_aeruginosa_strain_129980_chromosome_1,_c	(Newick)
CP195324.1_127552-128911_Pseudomonas_aeruginosa_strain_129284_ch	CP195324.1:127552-128911_Pseudomonas_aeruginosa_strain_129284_chromosome_1,_com	(Newick)
CP195324.1_128274-128330_Pseudomonas_aeruginosa_strain_129284_ch	CP195324.1:128274-128330_Pseudomonas_aeruginosa_strain_129284_chromosome_1,_com	(Newick)
CP195324.1_129414-129532_Pseudomonas_aeruginosa_strain_129284_ch	CP195324.1:129414-129532_Pseudomonas_aeruginosa_strain_129284_chromosome_1,_com	(Newick)
CP195324.1_6093128-6093319_Pseudomonas_aeruginosa_strain_129284	CP195324.1:6093128-6093319_Pseudomonas_aeruginosa_strain_129284_chromosome_1,_c	(Newick)
CP195324.1_885651-885842_Pseudomonas_aeruginosa_strain_129284_ch	CP195324.1:885651-885842_Pseudomonas_aeruginosa_strain_129284_chromosome_1,_com	(Newick)
HE583391.2_1-2102_Pseudomonas_aeruginosa_partial_class_I_integro	HE583391.2:1-2102_Pseudomonas_aeruginosa_partial_class_I_integron,_strain_AES83	(Newick)
HE583391.2_1933-1989_Pseudomonas_aeruginosa_partial_class_I_inte	HE583391.2:1933-1989_Pseudomonas_aeruginosa_partial_class_I_integron,_strain_AE	(Newick)
HE583391.2_727-783_Pseudomonas_aeruginosa_partial_class_I_integr	HE583391.2:727-783_Pseudomonas_aeruginosa_partial_class_I_integron,_strain_AES8	(Newick)
MK450539.1_15206-15394_Pseudomonas_aeruginosa_DIM-1_encoding_reg	MK450539.1:15206-15394_Pseudomonas_aeruginosa_DIM-1_encoding_region_genomic_seq	(Newick)
MK450539.1_57850-59209_Pseudomonas_aeruginosa_DIM-1_encoding_reg	MK450539.1:57850-59209_Pseudomonas_aeruginosa_DIM-1_encoding_region_genomic_seq	(Newick)
MK450539.1_58572-58628_Pseudomonas_aeruginosa_DIM-1_encoding_reg	MK450539.1:58572-58628_Pseudomonas_aeruginosa_DIM-1_encoding_region_genomic_seq	(Newick)
MK450539.1_59712-59830_Pseudomonas_aeruginosa_DIM-1_encoding_reg	MK450539.1:59712-59830_Pseudomonas_aeruginosa_DIM-1_encoding_region_genomic_seq	(Newick)