Generalized UniFrac Distances, Distance-Based Multivariate Methods and Feature-Based Univariate Methods for Microbiome Data Analysis R package GUniFrac version 1.9 CRAN Task View: Phylogenetics (https://CRAN.R-project.org/view=Phylogenetics) A suite of methods for powerful and robust microbiome data analysis including data normalization, data simulation, community-level association testing and differential abundance analysis. It implements generalized UniFrac distances, Geometric Mean of Pairwise Ratios (GMPR) normalization, semiparametric data simulator, distance-based statistical methods, and feature-based statistical methods. The distance-based statistical methods include three extensions of PERMANOVA: (1) PERMANOVA using the Freedman-Lane permutation scheme, (2) PERMANOVA omnibus test using multiple matrices, and (3) analytical approach to approximating PERMANOVA p-value. Feature-based statistical methods include linear model-based methods for differential abundance analysis of zero-inflated high-dimensional compositional data. Software Depends: R (>= 3.5.0) Imports: Rcpp (>= 0.12.13), vegan, ggplot2, matrixStats, Matrix, ape, parallel, stats, utils, statmod, rmutil, dirmult, MASS, ggrepel, foreach, modeest, inline, methods LinkingTo: Rcpp Suggests: ade4, knitr, markdown, ggpubr Jun Chen <chen.jun2@mayo.edu> Comprehensive R Archive Network (CRAN) Jun Chen [aut, cre], Xianyang Zhang [aut], Lu Yang [aut], Lujun Zhang [aut] GPL-3 2025-08-25 application/tgz https://CRAN.R-project.org/package=GUniFrac doi:10.32614/CRAN.package.GUniFrac