XPHenry/Netfrac: Netfrac - Community distance calculation within sequence similarity networks

The NetFrac package allows the users to calculate the eight following network measures: NetUniFrac, Motifs, Spp, Spep, Spelp, Spinp distances and the Transfer index (two variants), between species communities present in a given sequence similarity network. The shortest path in a phylogenetic tree is traditionally used to estimate evolutionary distances between species. However, the shortest path concept can be extended to sequence similarity networks. The five following distances (NetUniFrac, Spp, Spep, Spelp, and Spinp) can be seen as network analogues of the traditional UniFrac distance used to assess distances between species communities in a phylogenetic tree, whereas the Transfer index is designed for estimating the rate and direction of horizontal gene transfers, or species dispersal, between different phylogenetic, or ecological, species communities.

Getting started

Package details

AuthorXing, Henry; Kembel, Steven W.; Makarenkov, Vladimir
MaintainerHenry Xing <xing.henry@courrier.uqam.ca>
LicenseGNU General Public License
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
XPHenry/Netfrac documentation built on Jan. 29, 2020, 12:14 p.m.