References

This page lists useful links and references that can help you in any way to improve your experience with CompPhy.

Softwares used & documentation

  • ScripTree: used to generate the trees. Check its website for more information about its syntax etc. May be needed for the manual tuning of the picture functionnality.

    ScripTree: scripting phylogenetic graphics François Chevenet, Olivier Croce, Maxime Hebrard, Richard Christen and Vincent Berry Bioinformatics 2010 26(8):1125-1126.

  • PAUP*: used for its MAST (Maximum Agreement SubTree) functionnalit and for computing the parsimonious trees (in the MRP supertree method).

    Swofford, D. L. 2003. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.

  • PHYLIP package: used for distance computation between two trees. The tool used in the package for this is Treedist (with the "symmetric difference" option).

    Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle.

  • Python library : Spruce library proposed by Rahul Suri and Tandy Warnow, making use of Thomas Mailund's open source newick parser. 

Links

Finding phylogenies

  • PhyloExplorer: check phylogenetic trees, get statistics, and many other functionnalities.
  • TreeBASE: a relational database designed to manage and explore information on phylogenetic relationships.
  • Tree of Life: navigate and retrieve information from the tree of life.
  • NCBI taxonomy: taxonomy resources, statistics, etc.