PyPhy: A phylogenomic approach to microbial evolution
Sicheritz-Ponten T, Andersson SG: Nucleic Acids Res. 2001 Jan 15;29(2):545-52.
We are currently working on SPyPhy -
the next generation of PyPhy.
Therefore, all PyPhy development has been
What is PyPhy ?
PyPhy is a set of python scripts and modules for automatic, large-scale
reconstructions of phylogenetic relationships of complete microbial
genomes. PyPhy 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 Maps for a
How should I cite PyPhy ?
A phylogenomic approach to microbial evolution
Sicheritz-Ponten T, Andersson SG: Nucleic Acids Res. 2001 Jan
Are there any screenshots ?
Of course we have screenshots ...
Take a look at following Phylome
Where can I get the latest version of PyPhy ?
PyPhy code may be obtained from the
authors on request.
What do I need to run PyPhy ?
Take a look at our requirements page.
How do I set up PyPhy ?
Documentation how to set up PyPhy follows with the distribution.
You need to have a minimal knowledge of how to administrate a
UNIX-like system and probably you'll need root access.
How do I report bugs ?
I am continuing development as I find time, so YOUR input is
Please mail any suggestions, observations to Thomas Sicheritz-PontÚn
How fast is PyPhy ?
Generating all phylogenetic trees for a typical bacterial genome
would take 1-2 hours on our 32 processor IRIX machine and ca. one
week on my laptop (PII 300Mz, running SuSE Linux)
- Added an Annotator
- Added a Report generator
- Added TNG analysis
- Added paralogue collector
- Added Wheel-zooming for Phylomes
- Added TNG MrBayes analysis
- Added replicates remover
- Added Atlas-view
- Added UserTags, UserAnnotations and annotation-infos
- Added GBlocks for alignment cleaning
- Moved more code into BioPython
- Started automagic annotation
- Improved the handling of names vs. aliases
- Added additional dictionary for lost embl entries
- Rewrote the whole phylogenomic connection part, added Get_All_Connections
- Added support for multiple databases
- Added array view for EST projects
- It is possible to include the FASTA infile in the database
(usefull for complete genome analysis)
- Added detailed html output
- Added EST support
- Added Seed option for EST DNA Data
- Changed Nr to phyphynr
- Added Postscript output
- Added more Search functions
What else is planned for PyPhy ?
- Support for EST projects (Status: finished)
- Support formultiple databases (Status: beta, working)
- Support for ongoing genome sequencing projects (Status: beta, working)
- HTML first scan output (Status: finished)
- Support for multi-processors (Status: finished)
- Include alignment optimizer (ASRM) (Status: brainstorming - sugesstions welcome)
- Refine phylogenetic methods (Status: brainstorming - sugesstions welcome)
- Refine selection procedure (Status: brainstorming - sugesstions welcome)
- Create Phylome map of A.thaliana (Status: completed)
- Link Phylome Maps to Genome Atlas (Status: beta, working)
Thomas Sicheritz <email@example.com>
Last modified: Thu Aug 11 15:11:06 MDT 2005