PyPhy: A phylogenomic approach to microbial evolution

We are currently working on SPyPhy - the next generation of PyPhy.
Therefore, all PyPhy development has been discontinued.

• 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 microbial genome.

• How should I cite PyPhy ?

  A phylogenomic approach to microbial evolution
  Sicheritz-Ponten T, Andersson SG: Nucleic Acids Res. 2001 Jan 15;29(2):545-52.

• Are there any screenshots ?

  Of course we have screenshots ...
  Take a look at following Phylome Maps ...
  • Phylome Map of R.prowazekii
  • Phylome Map of R.prowazekii connected to the KEGG database, showing tRNA-syntethase genes
  • Phylome Map of R.prowazekii suggesting a horizontal gene transfer event in the Lysine tRNA-syntethase tree
  • Lysine tRNA-syntethase tree automatically switching the geneID to organism names and gene names
  • T.maritima
  • P.abyssi
  • M.janaschii
  • B.burgerdorfii
  • A.aeolicus
  • Synechocystis
  • C.pneumonia

• 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 valuable.
  Please mail any suggestions, observations to Thomas Sicheritz-Pontén

• 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)

• Recent Changes

  • 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)

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  Thomas Sicheritz <thomas@cbs.dtu.dk>
  Last modified: Thu Aug 11 15:11:06 MDT 2005