Lab meeting tuesday February 5th 2013

Dongying Wu will be presenting for this week’s lab meeting.
the title of the talk is “Taxonomic Classification based on Phylogenetic Trees”.
We will be meeting at the Genome Center from 1:30 to 3:00pm in room 4202.

Author: gjospin

Bioinformatics Engineer in Dr. Jonathan Eisen's lab at UCDavis.

One thought on “Lab meeting tuesday February 5th 2013”

  1. Notes for meeting:

    Lab business:
    * Trying to coordinate DNA extraction kits across multiple projects.
    * Merlot is back online.

    Dongying Wu presentation on Taxonomic Classification Based on Phylogenetic Trees

    * How to calculate which clades in different parts of a tree should be considered the same level?
    * Developed formula to calculate depth in a tree for different nodes
    * What is the cutoff to use for “species”? (or for a 97% cutoff) 16S alignment
    *Calculate clusters with Mothur with 97% cutoff
    *Then compare to tree-D based clusters

    * How to compare two clusters
    * counting pairs
    * overlapping analysis
    * variation of information

    * Did this for rRNA trees
    * Compare MI for tree D clusters vs. MOTHUR clusters

    * Did this for protein trees for all genomes

    * Did this for two trees


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