Equipe MAB - LIRMM Information Genomique et Structurale
A new version of phylogeny.fr is available.
Please try it: NGphylogeny.fr.
"One Click" Mode
Alignment
MUSCLESettings:
Run mode: full processing mode
 doc
->
Phylogeny
PhyMLSettings:
Model: Default
Statistical test: alrt
Number of categories: 4
Gamma: estimated
Invariable sites: estimated
 doc
->
Tree Rendering
TreeDynSettings:
Conformation: rectangular
Legend: displayed
Branch annotation: bootstrap
Font: Times 10 normal
 doc
Alignment
MUSCLESettings:
Run mode: full processing mode
 doc
->
Curation
GblocksSettings:
Min. seq. for flank pos.: 85%
Max. contig. nonconserved pos.: 8
Min. block length: 10
Gaps in final blocks: no
 doc
->
Phylogeny
PhyMLSettings:
Model: Default
Statistical test: alrt
Number of categories: 4
Gamma: estimated
Invariable sites: estimated
 doc
->
Tree Rendering
TreeDynSettings:
Conformation: rectangular
Legend: displayed
Branch annotation: bootstrap
Font: Times 10 normal
 doc
Help ?


Name of the analysis Name length is limited to 20 characters (optional):

Upload your set of sequences in FASTA, EMBL or NEXUS format from a file:

Or paste it here (load example of sequences)

Maximum number of sequences is 200 for proteins and 200 for nucleic acids.
Maximum length of sequences is 2000 for proteins and 6000 for nucleic acids.

Names associationOptionally, you can specify the association between truncated taxon names (used in input data) and original long taxon names (human readable). Each short name of a line on the left will be associated to the long name of the corresponding line on the right.
Note: line numbers leading each line will be automatically removed, don't worry about them.
Short names used in input dataShort names are the names used in the input data. Usually, theses names are short and only contain valid characters (no spaces, quotes and such).
Note: a short name must be associated to one and only one long name.		 Real long names (human readable)Long names are explicit taxon names with unlimited length and can contain special characters.

Use the Gblocks program to eliminate poorly aligned positions and divergent regions

email: To receive the results by e-mail, enter your address(es)Multiple e-mail addresses can be entered separated by spaces, semicolon or comma.:
Do not attach result files




Note: beside sequences count and average length limit for the alignment stage there is also a limitation on the phylogeny stage (sequences_count*sequences_count*aligned_sequence_length=100000000) that will be checked once the alignment is done.

Note: usual bootstrapping procedure is replaced by a new confidence index that is much faster to compute.
See 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) for details.

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