Cite & Contact
Prokaryotes Phylogeny Facility - PPF
QUERY with possible recruitment of the most similar sequences
accession nos. (ex: #AB681800 @superstringent %tag) OR name(s) (ex #Sodalis_praecaptivus @superstringent %notag)
OR sequences in fasta format (no extraction to do => no database to indicate, no tag to choose)
DB selection for extraction: @database with @[lax, stringent, TS-stringent, superstringent, genuslevel]. Tagging: %[tag, notag]
When submitting a mix of the query styles, the # containing selection rule must be AT THE BEGINNING
Large phylogenies (N>1000) may be long or very long to compute. PPF is more adapted to study relatively close phylogenetic relationships.
Blast parameters used for recruitment of similar sequences
Max # of BLAST hits to align :
to suppress recruitment)
[upper bound on the expected frequency of chance occurrence of a set of HSPs (-e)]
Sequence Database used for the recruitment of similar sequences
(last updated 2018/Oct/06 - SSU/LSU V37n (new construction engine) CDS V37o (old way))
Note that the "lax" database is
recommended to recruit proximal sequences to the query,
please use it only with a limited number of sequences !
Supplemental Query without recruitment
With the same grammar as above you may submit a request but the most similar sequences will not be recruited.
This may be usefull to recognize some sequences as an external group.
use here the "lax" database as target for extraction ("@lax"), this huge database is not strand-homogeneous and must be treated on the fly to find the strand.
User-given Id. :
Max length of sequence names
[The shorter the name the cleaner the tree, pay attention to the remaining discrimination power]
Build phylogenetic tree
Build tree for each sequence
[You may use "Yes" if your input data contain phylogenetically distant sequences]
Depending the program, the "accurency oriented" option may give the optimal alignment (and is always very slow).
Selection of phylogenetically informative regions
No post-processing of the alignment (better if closely related sequences)
Results will not be conserved for more than 18 hours, if needed please
your working directory by using the
link and selecting the leBIBIdatas.tar file