Generalized UniFrac

eagle-i ID

Resource Type

Properties

1. Resource Description

   The human microbiome plays an important role in human disease and health. Identification of factors that affect the microbiome composition can provide insights into disease mechanism as well as suggest ways to modulate the microbiome composition for therapeutical purposes. Distance-based statistical tests have been applied to test the association of microbiome composition with environmental or biological covariates. The unweighted and weighted UniFrac distances are the most widely used distance measures. However, these two measures assign too much weight either to rare lineages or to most abundant lineages, which can lead to loss of power when the important composition change occurs in moderately abundant lineages. We develop generalized UniFrac distances that extend the weighted and unweighted UniFrac distances for detecting a much wider range of biologically relevant changes.

2. Additional Name

   GUniFrac

3. Used by

   Statistical Genetics and Genomics Laboratory

4. Version

   1.0

5. Data Input

   Rooted phylogenetic tree of R class "phylo"

6. Data Input

   Operational taxonomic unit count table

7. Data Output

   Generalized UniFrac distances

8. Related Publication or Documentation

   Associating microbiome composition with environmental covariates using generalized UniFrac distances

9. Website(s)

   http://cran.r-project.org/web/packages/GUniFrac/index.html

10. Related Technique

    Metagenomics analysis

11. Developed by

    Li, Hongzhe., PhD

12. Software license

    GNU General Public License

13. Coded in

    R language