PhyloSift website updates

General questions:

  • What are our “levels” of PhyloSift markers – need to standardize terminology
    • “elite markers” – only DNGNGWU?
    • “core markers” – all devel markers?
    • “extended markers” – protein families; additional download
  • What is the ‘web’ folder that now appears in PS download folder?  – Eric’s scripts; Aaron will remove.
  • Still finding the –help dialogue flag structure really confusing. These do nothing: commands: list the application’s commands help: display a command’s help screen

Intro Tutorial – web updates needed

  • Update screenshot of output directory with newest collection of output files
  • Update the names of the krona files that get generated in the output directory
  • Add info about the automatic fat tree visualization that Aaron just added to outputs

Bayes factor tests – new page creation

  • Screenshot of equation used
  • Explanation about what Bayes factor tests do
  • Commands/workflow needed to run Bayes factor tests
  • How to interpret the outputs generated – biological context, uncertainty/detection thresholds

Output files – major page update

  • Go through outputs from HMP data and update and explain new file types

General Web Updates

  • Check all pages to make sure double dashes are inserted – Done already – Intro tutorial, phylosift RC file page, Monkey, Kangaroo, DBupdate
  • Update example command lines on Monkey, Kangaroo, DBupdate (e.g. with new flag structure). Done- 11/9/12
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