Phylogenetic analysis

GeneStudio's Phylogeny interface makes the performance and management of Phylogenetic analyses faster and more convenient.  GeneStudio's phylogeny tools include fastDNAml, a subset of programs from the PHYLIP suite, and TREE-PUZZLE.  Phylogeny results created using GeneStudio are stored in a database, and can be retrieved and managed using GeneStudio's Phylogeny results browser.

All of GeneStudio's phylogeny programs dialog boxes include an Analysis title.  This title is used to identify the stored results for future viewing, and should be descriptive.  Results of each analysis are stored in your [APPLICATION DATA] folder, in the GeneStudio\Phylogeny subfolder.  The value of [APPLICATION DATA] varies, but a typical path would be C:\Documents and Settings\User name\Application Data\.  Results can be retrieved for later viewing using GeneStudio's Phylogeny results browser.

Note: GeneStudio replaces the command line interface of these programs with a convenient and user-friendly dialog-box interface.  Understanding the details of each dialog will require careful reading of the documentation for each program.  Before using any of the phylogeny analysis programs, please visit the following web sites for more information:

PHYLIP: http://evolution.genetics.washington.edu/phylip.html
fastDNAml: http://geta.life.uiuc.edu/~gary/programs/fastDNAml.html
TREE-PUZZLE: http://www.tree-puzzle.de/
 


Programs

fastDNAml package: fastDNAml, and Windows implementation of the fastDNAml_boot as well as the fastDNAml_loop scripts
PHYLIP package: DNADIST/NEIGHBOR, DNAML, DNAPARS
TREE-PUZZLE: Quartet puzzling, tree reconstruction using pairwise comparison and user defined trees

Where appropriate, related programs are coordinated. For example, when PHYLIP's DNAML is run with the bootstrapping option selected, GeneStudio automatically processes the alignment with SEQBOOT, then DNAML, and finally CONSENSE.

The flow of program coordination is as follows:

DNADIST >> NEIGHBOR
or when the Bootstraps option is selected
SEQBOOT >> DNADIST >> NEIGHBOR >> CONSENSE

DNAML
or when the Bootstraps option is selected
SEQBOOT >> DNAML >> CONSENSE

DNAPARS
or when the Bootstraps option is selected
SEQBOOT >> DNAPARS >> CONSENSE

fastDNAml
or
fastDNAml_loop script implementation
or
fastDNAml_boot script implementation >> CONSENSE

Notes:

  1. The PHYLIP package is not distributed with GeneStudio.  When you run a PHYLIP function for the first time, you will be prompted for the location of the programs from the PHYLIP package.  A download link is provided if they are not installed on your computer.
  2. fastDNAml_boot and fastDNAml_loop were originally implemented by Gary J. Olsen as UNIX shell scripts which do not run in Windows.  GeneStudio includes a new implementation of these algorithms specifically written to run in Windows.

Viewing results

Output files from phylogenetic analyses are automatically loaded into the Phylogeny viewer on completion. The viewer includes a drop-down list for the selection of different output files. When a tree is displayed, a link to the popular program TreeView by Rod Page is activated.  Pressing the TreeView button launches TreeView with the tree file loaded.  Stored results can be displayed using GeneStudio's Phylogeny results viewer.  To launch the phylogeny results browser, press the button on the toolbar, or select Phylogeny results browser from the Phylogeny menu.

The Phylogeny results browser displays a list including the analysis title, date and time, and programs used.  To open an analysis, click on the entry in the list, then press the Open button.  To view detailed information about the selected analysis, press the summary button.  To delete an analysis, press the Deletebutton. 

Note: The first time TreeView is used, GeneStudio will display a prompt for the program location.  A download link is provided if TreeView is not installed.
 


Recommended reading:

  1. Claverie J, Notredame C. Bioinformatics for Dummies. Indianapolis, IN: Wiley Publishing, Inc.; 2003.
  2. Felsenstein J. Inferring Phylogenies. Sunderland, MA: Sinauer Associates, Inc.; 2003.
  3. Hall BG. Phylogenetic Trees Made Easy. Sunderland, MA: Sinauer Associates, Inc.; 2001.
  4. Hillis DM, Moritz C, Mable BK, editors. Molecular Systematics, 2nd Edition. Sunderland, MA: Sinauer Associates, Inc.; 1996.
  5. Krawetz SA, Womble DD. Introduction to Bioinformatics. Totowa, NJ: Humana Press; 2003.
  6. Swofford DL, Olsen GJ, Waddell PJ, Hillis DM. Phylogenetic Inference. In: Molecular Systematics. Edited by Hillis DM, Moritz C, Mable BK. Sunderland, Massachusetts: Sinauer Associates, Inc.; 1996:407-514.