SPyPhy: A (spying) phylogenomic approach to genome evolution
(or the sequel to PyPhy)
Sicheritz-Ponten T, Alsmark C, Hirt R, Embley TM - unpublished
What is SPyPhy ?
SPyPhy is the next generation of PyPhy - a set of python scripts
and modules for automatic, large-scale reconstructions of
phylogenetic relationships of complete genomes. SPyPhy
consists of AutoTree which
automatically generates phylogenetic trees for each amino acid
sequence in a FASTA file, and Xphylome which generates and
visualizes the Phylome Grids for a
microbial or eukaryote genome. (completed, unfinished or EST)
Where can I get the latest version of SPyPhy ?
SPyPhy is tightly integrated in our genome and neural network
pipelines and can therefore not be easily distributed. You can, however,
suggest a collaboration on interesting genomes.
For commercial licences, send inquiries by e-mail to firstname.lastname@example.org
What is the difference between SPyPhy and PyPhy?
SPyPhy can (as PyPhy) automatically generate phylogenetic trees from
complete (or partial) genome sequences. SPyPhy is a complete
rewrite of the PyPhy code which makes it much faster and tends to give
better trees. As SPyPhy is build around an SQL engine it can handle
multiple genomes and uses information across different
phylomes. (Spy mode)
- SQL based engine
- Faster and can handle huge genomes
- P4 based tree handling
- Spy mode
- A completely new and more powerfull
automated annotator and reporter function.
- Integrated colored KEGG view for all genes with automatically annotated EC numbers.
- Integrated neural network based ranking of HGT's.
- Builtin tutorials and notes.
- Zoom of grid and trees.
- Integrated support for MrBayes (TNG analysis).
- Integrated protein-protein interaction prediction.
- Muscle, Clustalw and MAFFT alignments
Thomas Sicheritz <email@example.com>
Last modified: Wed Apr 2 20:38:28 CEST 2008