SPyPhy: A (spying) phylogenomic approach to genome evolution
(or the sequel to PyPhy)

• 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 software@cbs.dtu.dk

• 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