R Package Scholar
27,143
Referenced by ⇅ Year
ACDC: Analysis of Congruent Diversification Classes (Version 1.0.0)

2022
apTreeshape: Analyses of Phylogenetic Treeshape (Version 1.5-0.1)

2005
BayesSPsurv: Bayesian Spatial Split Population Survival Model (Version 0.1.4)

2020
brranching: Fetch "Phylogenies" from Many Sources (Version 0.7.0)

2015
dcGOR: Analysis of Ontologies and Protein Domain Annotations (Version 1.0.6)

2014
ggmotif: Extract and Visualize Motif Information from MEME Software (Version 0.2.1)

2021
HierDpart: Partitioning Hierarchical Diversity and Differentiation Across Metrics and Scales, from Genes to Ecosystems (Version 1.5.0)

2018
liayson: Linking Singe-Cell Transcriptomes Atween Contemporary Subpopulation Genomes (Version 1.0.5)

2018
perfectphyloR: Reconstruct Perfect Phylogenies from DNA Sequence Data (Version 0.2.1)

2019
PIGShift: Polygenic Inverse Gamma Shifts (Version 1.0.1)

2014
pirouette: Create a Bayesian Posterior from a Phylogeny (Version 1.6.9)

2022
prewas: Data Pre-Processing for Bacterial Genome-Wide Association Studies (Version 1.1.1)

2020
Rarefy: Rarefaction Methods (Version 1.1.1)

2020
safedata: Interface to Data from the SAFE Project (Version 1.1.3)

2020
subniche: Within Outlying Mean Indexes: Refining the OMI Analysis (Version 1.5)

2016
treeducken: Nested Phylogenetic Tree Simulator (Version 1.1.0)

2020
treeplyr: "dplyr" Functionality for Matched Tree and Data Objects (Version 0.1.10)

2016
sandwichr: Spatial Interpolation Based on Spatial Stratified Heterogeneity (Version 1.0.4)

2022
PhyInsight: DNA Sequence Analysis & Generation Tree Creation (Version 0.1.0)

2023
StructFDR: False Discovery Control Procedure Integrating the Prior Structure Information (Version 1.4)

2016
changeRangeR: Change Metrics for Species Geographic Ranges (Version 1.1.0)

2022
bite: Bayesian Integrative Models of Trait Evolution (Version 0.3)

2020
treedata.table: Manipulation of Matched Phylogenies and Data using 'data.table' (Version 0.1.0)

2020
datelife: Scientific Data on Time of Lineage Divergence for Your Taxa (Version 0.6.8)

2022
refdb: A DNA Reference Library Manager (Version 0.1.1)

2022
OpenTreeChronograms: Open Tree of Life Chronograms (Version 2022.1.28)

2022
metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data (Version 0.3.7)

2016
GaMaBioMD: Diversity Analysis for Sequence Data (Version 0.2.0)

2024
taxize: Taxonomic Information from Around the Web (Version 0.9.100.1)

2012
autoGO: Auto-GO: Reproducible, Robust and High Quality Ontology Enrichment Visualizations (Version 0.9.1)

2023
qlcData: Processing Data for Quantitative Language Comparison (Version 0.3)

2015
Anaconda: Targeted Differential and Global Enrichment Analysis of Taxonomic Rank by Shared Asvs (Version 0.1.5)

2022
AnnotationBustR: Extract Subsequences from GenBank Annotations (Version 1.3.0)

2017
Apoderoides: Prioritize and Delete Erroneous Taxa in a Large Phylogenetic Tree (Version 3.0.0)

2024
BAMMtools: Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees (Version 2.1.12)

2014
BAT: Biodiversity Assessment Tools (Version 2.9.6)

2014
BIEN: Tools for Accessing the Botanical Information and Ecology Network Database (Version 1.2.6)

2017
BSTZINB: Association Among Disease Counts and Socio-Environmental Factors (Version 1.0.1)

2024
BarcodingR: Species Identification using DNA Barcodes (Version 1.0-3)

2016
BoSSA: A Bunch of Structure and Sequence Analysis (Version 3.7)

2009
CALANGO: Comparative Analysis with Annotation-Based Genomic Components (Version 1.0.20)

2021
CRABS: Congruent Rate Analyses in Birth-Death Scenarios (Version 1.2.0)

2022
CTNote: CTN Outcomes, Treatments, and Endpoints (Version 0.1.0)

2022
Canopy: Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing (Version 1.3.0)

2015
Claddis: Measuring Morphological Diversity and Evolutionary Tempo (Version 0.7.0)

2015
CommEcol: Community Ecology Analyses (Version 1.8.1)

2016
CongreveLamsdell2016: Distance Metrics for Trees Generated by Congreve and Lamsdell (Version 1.0.3)

2019
DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction (Version 4.4.1)

2015
DAISIEprep: Extracts Phylogenetic Island Community Data from Phylogenetic Trees (Version 0.4.0)

2023
DAMOCLES: Dynamic Assembly Model of Colonization, Local Extinction and Speciation (Version 2.3)

2014
DCLEAR: Distance Based Cell Lineage Reconstruction (Version 1.0.13)

2021
DDD: Diversity-Dependent Diversification (Version 5.2.2)

2012
DHARMa: Residual Diagnostics for Hierarchical (Multi-Level / Mixed) Regression Models (Version 0.4.7)

2016
ENMTools: Analysis of Niche Evolution using Niche and Distribution Models (Version 1.1.2)

2020
EnvNJ: Whole Genome Phylogenies Using Sequence Environments (Version 0.1.3)

2021
EpiModel: Mathematical Modeling of Infectious Disease Dynamics (Version 2.5.0)

2013
EvoPhylo: Pre- And Postprocessing of Morphological Data from Relaxed Clock Bayesian Phylogenetics (Version 0.3.2)

2022
FD: Measuring Functional Diversity (FD) from Multiple Traits, and Other Tools for Functional Ecology (Version 1.0-12.3)

2009
FinePop: Fine-Scale Population Analysis (Version 1.5.2)

2016
FishPhyloMaker: Phylogenies for a List of Finned-Ray Fishes (Version 0.2.0)

2021
FossilSim: Simulation and Plots for Fossil and Taxonomy Data (Version 2.4.1)

2018
FuncDiv: Compute Contributional Diversity Metrics (Version 1.0.0)

2023
GIFT: Access to the Global Inventory of Floras and Traits (GIFT) (Version 1.3.2)

2023
GLSME: Generalized Least Squares with Measurement Error (Version 1.0.5)

2014
GOCompare: Comprehensive GO Terms Comparison Between Species (Version 1.0.2.1)

2021
GUniFrac: Generalized UniFrac Distances, Distance-Based Multivariate Methods and Feature-Based Univariate Methods for Microbiome Data Analysis (Version 1.8)

2012
HACSim: Iterative Extrapolation of Species' Haplotype Accumulation Curves for Genetic Diversity Assessment (Version 1.0.6-1)

2019
HMPTrees: Statistical Object Oriented Data Analysis of RDP-Based Taxonomic Trees from Human Microbiome Data (Version 1.4)

2011
HSAUR: A Handbook of Statistical Analyses Using R (1st Edition) (Version 1.3-10)

2006
HSAUR2: A Handbook of Statistical Analyses Using R (2nd Edition) (Version 1.1-20)

2009
HSAUR3: A Handbook of Statistical Analyses Using R (3rd Edition) (Version 1.0-15)

2014
HTSSIP: High Throughput Sequencing of Stable Isotope Probing Data Analysis (Version 1.4.1)

2016
Hmsc: Hierarchical Model of Species Communities (Version 3.0-13)

2019
HybridMicrobiomes: Analysis of Host-Associated Microbiomes from Hybrid Organisms (Version 0.1.1)

2023
JNplots: Visualize Outputs from the 'Johnson-Neyman' Technique (Version 0.1.1)

2023
LorMe: Lightening One-Code Resolving Microbial Ecology Solution (Version 1.1.0)

2024
MACER: Molecular Acquisition, Cleaning, and Evaluation in R 'MACER' (Version 0.2.1)

2021
MAGNAMWAR: A Pipeline for Meta-Genome Wide Association (Version 2.0.4)

2017
MCMCglmm: MCMC Generalised Linear Mixed Models (Version 2.36)

2009
MCMCtreeR: Prepare MCMCtree Analyses and Plot Bayesian Divergence Time Analyses Estimates on Trees (Version 1.1)

2019
ML.MSBD: Maximum Likelihood Inference on Multi-State Trees (Version 1.2.1)

2017
MLVSBM: A Stochastic Block Model for Multilevel Networks (Version 0.2.4)

2021
MPSEM: Modelling Phylogenetic Signals using Eigenvector Maps (Version 0.5-1)

2013
MSCquartets: Analyzing Gene Tree Quartets under the Multi-Species Coalescent (Version 3.0)

2019
MSCsimtester: Tests of Multispecies Coalescent Gene Tree Simulator Output (Version 1.0.0)

2021
MVA: An Introduction to Applied Multivariate Analysis with R (Version 1.0-8)

2011
MiSPU: Microbiome Based Sum of Powered Score (MiSPU) Tests (Version 1.0)

2016
MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis (Version 0.10.1)

2024
MonoPhy: Explore Monophyly of Taxonomic Groups in a Phylogeny (Version 1.3.2)

2015
NST: Normalized Stochasticity Ratio (Version 3.1.10)

2019
NicheBarcoding: Niche-model-Based Species Identification (Version 1.0)

2021
OUwie: Analysis of Evolutionary Rates in an OU Framework (Version 2.10)

2011
OptCirClust: Circular, Periodic, or Framed Data Clustering: Fast, Optimal, and Reproducible (Version 0.0.4)

2020
PBD: Protracted Birth-Death Model of Diversification (Version 1.4)

2014
PCMBase: Simulation and Likelihood Calculation of Phylogenetic Comparative Models (Version 1.2.14)

2018
PCPS: Principal Coordinates of Phylogenetic Structure (Version 1.0.7)

2014
POMS: Phylogenetic Organization of Metagenomic Signals (Version 1.0.1)

2022
POSTm: Phylogeny-Guided OTU-Specific Association Test for Microbiome Data (Version 1.4)

2021
POUMM: The Phylogenetic Ornstein-Uhlenbeck Mixed Model (Version 2.1.7)

2017
PVR: Phylogenetic Eigenvectors Regression and Phylogentic Signal-Representation Curve (Version 0.3)

2012
PhySortR: A Fast, Flexible Tool for Sorting Phylogenetic Trees (Version 1.0.8)

2015
PhylogeneticEM: Automatic Shift Detection using a Phylogenetic EM (Version 1.7.0)

2017
Plasmidprofiler: Visualization of Plasmid Profile Results (Version 0.1.6)

2017
Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis (Version 3.6.0)

2021
Quartet: Comparison of Phylogenetic Trees Using Quartet and Split Measures (Version 1.2.7)

2019
RAINBOWR: Genome-Wide Association Study with SNP-Set Methods (Version 0.1.35)

2019
RNeXML: Semantically Rich I/O for the 'NeXML' Format (Version 2.4.11)

2014
RPANDA: Phylogenetic ANalyses of DiversificAtion (Version 2.3)

2014
RPointCloud: Visualizing Topological Loops and Voids (Version 0.8.0)

2024
RRPP: Linear Model Evaluation with Randomized Residuals in a Permutation Procedure (Version 2.0.3)

2018
RRphylo: Phylogenetic Ridge Regression Methods for Comparative Studies (Version 2.8.1)

2018
RVAideMemoire: Testing and Plotting Procedures for Biostatistics (Version 0.9-83-7)

2011
RevGadgets: Visualization and Post-Processing of 'RevBayes' Analyses (Version 1.2.1)

2021
Revticulate: Interaction with "RevBayes" in R (Version 1.0.0)

2021
Rogue: Identify Rogue Taxa in Sets of Phylogenetic Trees (Version 2.1.6)

2021
Rphylopars: Phylogenetic Comparative Tools for Missing Data and Within-Species Variation (Version 0.3.10)

2015
Rtapas: Random Tanglegram Partitions (Version 1.2)

2022
Rtropical: Data Analysis Tools over Space of Phylogenetic Trees Using Tropical Geometry (Version 1.2.1)

2021
SPARTAAS: Statistical Pattern Recognition and daTing using Archaeological Artefacts assemblageS (Version 1.2.4)

2021
STEPCAM: ABC-SMC Inference of STEPCAM (Version 1.2)

2014
STraTUS: Enumeration and Uniform Sampling of Transmission Trees for a Known Phylogeny (Version 1.1.2)

2019
SeqFeatR: A Tool to Associate FASTA Sequences and Features (Version 0.3.1)

2014
Seurat: Tools for Single Cell Genomics (Version 5.1.0)

2017
SiPhyNetwork: A Phylogenetic Simulator for Reticulate Evolution (Version 1.1.0)

2022
SigTree: Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree (Version 1.10.6)

2013
SoilTaxonomy: A System of Soil Classification for Making and Interpreting Soil Surveys (Version 0.2.4)

2021
Sysrecon: Systematical Metabolic Reconstruction (Version 0.1.3)

2022
TBRDist: Rearrangement Distances Between Unrooted Phylogenetic Trees (Version 1.0.2)

2020
TESS: Diversification Rate Estimation and Fast Simulation of Reconstructed Phylogenetic Trees under Tree-Wide Time-Heterogeneous Birth-Death Processes Including Mass-Extinction Events (Version 2.1.2)

2012
TML: Tropical Geometry Tools for Machine Learning (Version 2.3.0)

2023
TextMiningGUI: Text Mining GUI Interface (Version 0.3)

2020
TiPS: Trajectories and Phylogenies Simulator (Version 1.2.3)

2021
TotalCopheneticIndex: Quantify the Balance of Phylogenetic Trees (Version 2.0.1)

2016
TransPhylo: Inference of Transmission Tree from a Dated Phylogeny (Version 1.4.5)

2020
TreeDiagram: Tree Diagram (Version 0.1.1)

2020
TreeDist: Calculate and Map Distances Between Phylogenetic Trees (Version 2.9.1)

2020
TreeSearch: Phylogenetic Analysis with Discrete Character Data (Version 1.5.1)

2017
TreeSim: Simulating Phylogenetic Trees (Version 2.4)

2010
TreeSimGM: Simulating Phylogenetic Trees under General Bellman Harris and Lineage Shift Model (Version 2.5)

2013
TreeTools: Create, Modify and Analyse Phylogenetic Trees (Version 1.12.0)

2019
VDJgermlines: Variable, Diversity and Joining Sequences from Various Species (Version 0.1)

2018
Xplortext: Statistical Analysis of Textual Data (Version 1.5.4)

2017
aPCoA: Covariate Adjusted PCoA Plot (Version 1.3)

2020
abdiv: Alpha and Beta Diversity Measures (Version 0.2.0)

2020
adaptiveGPCA: Adaptive Generalized PCA (Version 0.1.3)

2017
ade4: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences (Version 1.7-22)

2002
adegenet: Exploratory Analysis of Genetic and Genomic Data (Version 2.1.10)

2007
adephylo: Exploratory Analyses for the Phylogenetic Comparative Method (Version 1.1-16)

2009
adespatial: Multivariate Multiscale Spatial Analysis (Version 0.3-24)

2016
adiv: Analysis of Diversity (Version 2.2.1)

2017
admtools: Estimate and Manipulate Age-Depth Models (Version 0.4.0)

2023
alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis (Version 1.3.0)

2016
apex: Phylogenetic Methods for Multiple Gene Data (Version 1.0.6)

2015
aphid: Analysis with Profile Hidden Markov Models (Version 1.3.5)

2017
aphylo: Statistical Inference and Prediction of Annotations in Phylogenetic Trees (Version 0.3-3)

2022
aqp: Algorithms for Quantitative Pedology (Version 2.1.0)

2010
arakno: ARAchnid KNowledge Online (Version 1.3.0)

2021
asnipe: Animal Social Network Inference and Permutations for Ecologists (Version 1.1.17)

2016
avotrex: A Global Dataset of Anthropogenic Extinct Birds and their Traits: Phylogeny Builder (Version 1.3.0)

2024
babette: Control 'BEAST2' (Version 2.3.4)

2020
beastier: Call 'BEAST2' (Version 2.5.2)

2019
beautier: 'BEAUti' from R (Version 2.6.12)

2018
betapart: Partitioning Beta Diversity into Turnover and Nestedness Components (Version 1.6)

2012
bioregion: Comparison of Bioregionalisation Methods (Version 1.1.1)

2023
bioseq: A Toolbox for Manipulating Biological Sequences (Version 0.1.4)

2020
bivariatemaps: Creates Bivariate Maps (Version 1.7)

2022
bnpsd: Simulate Genotypes from the BN-PSD Admixture Model (Version 1.3.13)

2018
brms: Bayesian Regression Models using 'Stan' (Version 2.22.0)

2015
canaper: Categorical Analysis of Neo- And Paleo-Endemism (Version 1.0.1)

2022
caper: Comparative Analyses of Phylogenetics and Evolution in R (Version 1.0.3)

2011
castor: Efficient Phylogenetics on Large Trees (Version 1.8.2)

2017
cati: Community Assembly by Traits: Individuals and Beyond (Version 0.99.4)

2014
cauphy: Trait Evolution on Phylogenies Using the Cauchy Process (Version 1.0.3)

2023
chemodiv: Analysing Chemodiversity of Phytochemical Data (Version 0.3.0)

2022
cloneRate: Estimate Growth Rates from Phylogenetic Trees (Version 0.2.3)

2023
clue: Cluster Ensembles (Version 0.3-65)

2004
coalescentMCMC: MCMC Algorithms for the Coalescent (Version 0.4-4)

2012
coil: Contextualization and Evaluation of COI-5P Barcode Data (Version 1.2.4)

2019
colordistance: Distance Metrics for Image Color Similarity (Version 1.1.2)

2017
concatipede: Easy Concatenation of Fasta Sequences (Version 1.0.1)

2021
convevol: Analysis of Convergent Evolution (Version 2.2.1)

2013
copyseparator: Assembling Long Gene Copies from Short Read Data (Version 1.2.0)

2022
corHMM: Hidden Markov Models of Character Evolution (Version 2.8)

2013
covid19.analytics: Load and Analyze Live Data from the COVID-19 Pandemic (Version 2.1.3.3)

2020
ctpm: Continuous-Time Phylogenetic Modeling (Version 1.0.1)

2021
dartR.base: Analysing 'SNP' and 'Silicodart' Data - Basic Functions (Version 0.98)

2023
dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis (Version 2.9.7)

2017
data.tree: General Purpose Hierarchical Data Structure (Version 1.1.0)

2015
ddtlcm: Latent Class Analysis with Dirichlet Diffusion Tree Process Prior (Version 0.2.1)

2023
debar: A Post-Clustering Denoiser for COI-5P Barcode Data (Version 0.1.1)

2019
deeptime: Plotting Tools for Anyone Working in Deep Time (Version 2.1.0)

2021
dendextend: Extending 'dendrogram' Functionality in R (Version 1.18.1)

2014
dispRity: Measuring Disparity (Version 1.8)

2018
distory: Distance Between Phylogenetic Histories (Version 1.4.5)

2012
divent: Entropy Partitioning to Measure Diversity (Version 0.4-4)

2024
diversitree: Comparative 'Phylogenetic' Analyses of Diversification (Version 0.10-1)

2010
divraster: Diversity Metrics Calculations for Rasterized Data (Version 1.0.4)

2023
do3PCA: Probabilistic Phylogenetic Principal Component Analysis (Version 1.0.0)

2024
dowser: B Cell Receptor Phylogenetics Toolkit (Version 2.3)

2021
dynamicSDM: Species Distribution and Abundance Modelling at High Spatio-Temporal Resolution (Version 1.3.4)

2023
ecolottery: Coalescent-Based Simulation of Ecological Communities (Version 1.0.0)

2017
ecoregime: Analysis of Ecological Dynamic Regimes (Version 0.2.0)

2023
ecotraj: Ecological Trajectory Analysis (Version 0.1.1)

2021
ecospat: Spatial Ecology Miscellaneous Methods (Version 4.1.1)

2014
entropart: Entropy Partitioning to Measure Diversity (Version 1.6-15)

2013
enveomics.R: Various Utilities for Microbial Genomics and Metagenomics (Version 1.9.1)

2016
epm: EcoPhyloMapper (Version 1.1.3)

2022
evobiR: Comparative and Population Genetic Analyses (Version 1.1)

2013
evolqg: Evolutionary Quantitative Genetics (Version 0.3-4)

2015
evolvability: Calculation of Evolvability Parameters (Version 2.0.0)

2014
fido: Bayesian Multinomial Logistic Normal Regression (Version 1.1.1)

2022
file2meco: Transform Files to 'microtable' Object with 'microeco' Package (Version 0.9.0)

2021
fishtree: Interface to the Fish Tree of Life API (Version 0.3.4)

2018
funspace: Creating and Representing Functional Trait Spaces (Version 0.2.2)

2023
geiger: Analysis of Evolutionary Diversification (Version 2.0.11)

2007
genBaRcode: Analysis and Visualization Tools for Genetic Barcode Data (Version 1.2.7)

2017
geneHapR: Gene Haplotype Statistics, Phenotype Association and Visualization (Version 1.2.4)

2022
geomorph: Geometric Morphometric Analyses of 2D and 3D Landmark Data (Version 4.0.8)

2012
ggimage: Use Image in 'ggplot2' (Version 0.3.3)

2017
ggmuller: Create Muller Plots of Evolutionary Dynamics (Version 0.5.6)

2017
ggrasp: Gaussian-Based Genome Representative Selector with Prioritization (Version 1.2)

2018
glinvci: Phylogenetic Comparative Methods with Uncertainty Estimates (Version 1.2.4)

2021
glmmTMB: Generalized Linear Mixed Models using Template Model Builder (Version 1.1.10)

2017
gquad: Prediction of G Quadruplexes and Other Non-B DNA Motifs (Version 2.1-2)

2015
gromovlab: Gromov-Hausdorff Type Distances for Labeled Metric Spaces (Version 0.8-3)

2015
hagis: Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity (Version 3.1.12)

2019
haplotypes: Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony (Version 1.1.3.1)

2015
harmonicmeanp: Harmonic Mean p-Values and Model Averaging by Mean Maximum Likelihood (Version 3.0.1)

2017
harrietr: Wrangle Phylogenetic Distance Matrices and Other Utilities (Version 0.2.3)

2017
hierfstat: Estimation and Tests of Hierarchical F-Statistics (Version 0.5-11)

2004
hillR: Diversity Through Hill Numbers (Version 0.5.2)

2018
hilldiv: Integral Analysis of Diversity Based on Hill Numbers (Version 1.5.1)

2019
hisse: Hidden State Speciation and Extinction (Version 2.1.11)

2015
holobiont: Microbiome Analysis Tools (Version 0.1.2)

2024
homals: Gifi Methods for Optimal Scaling (Version 1.0-10)

2003
iCAMP: Infer Community Assembly Mechanisms by Phylogenetic-Bin-Based Null Model Analysis (Version 1.5.12)

2020
iCellR: Analyzing High-Throughput Single Cell Sequencing Data (Version 1.6.7)

2019
iNEXT.3D: Interpolation and Extrapolation for Three Dimensions of Biodiversity (Version 1.0.6)

2024
iNEXT.beta3D: Interpolation and Extrapolation with Beta Diversity for Three Dimensions of Biodiversity (Version 1.0.2)

2024
idar: Individual Diversity-Area Relationships (Version 1.5)

2017
igraph: Network Analysis and Visualization (Version 2.1.1)

2006
immunarch: Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires (Version 0.9.1)

2020
indelmiss: Insertion Deletion Analysis While Accounting for Possible Missing Data (Version 1.0.10)

2016
insect: Informatic Sequence Classification Trees (Version 1.4.2)

2018
ipADMIXTURE: Iterative Pruning Population Admixture Inference Framework (Version 0.1.0)

2020
ips: Interfaces to Phylogenetic Software in R (Version 0.0.12)

2014
itol.toolkit: Helper Functions for 'Interactive Tree Of Life' (Version 1.1.7)

2023
jSDM: Joint Species Distribution Models (Version 0.2.6)

2019
jackalope: A Swift, Versatile Phylogenomic and High-Throughput Sequencing Simulator (Version 1.1.5)

2019
jrich: Jack-Knife Support for Evolutionary Distinctiveness Indices I and W (Version 0.60-35)

2016
kmer: Fast K-Mer Counting and Clustering for Biological Sequence Analysis (Version 1.1.2)

2018
lingtypology: Linguistic Typology and Mapping (Version 1.1.20)

2016
longreadvqs: Viral Quasispecies Comparison from Long-Read Sequencing Data (Version 0.1.3)

2024
mFD: Compute and Illustrate the Multiple Facets of Functional Diversity (Version 1.0.7)

2021
markophylo: Markov Chain Models for Phylogenetic Trees (Version 1.0.9)

2015
mcbette: Model Comparison Using 'babette' (Version 1.15.3)

2020
mdendro: Extended Agglomerative Hierarchical Clustering (Version 2.2.1)

2018
meconetcomp: Compare Microbial Networks of 'trans_network' Class of 'microeco' Package (Version 0.5.1)

2022
mecoturn: Decipher Microbial Turnover along a Gradient (Version 0.3.0)

2023
metadat: Meta-Analysis Datasets (Version 1.2-0)

2021
metafor: Meta-Analysis Package for R (Version 4.6-0)

2009
metagear: Comprehensive Research Synthesis Tools for Systematic Reviews and Meta-Analysis (Version 0.7)

2015
microeco: Microbial Community Ecology Data Analysis (Version 1.10.0)

2020
mmodely: Modeling Multivariate Origins Determinants - Evolutionary Lineages in Ecology (Version 0.2.5)

2022
motmot: Models of Trait Macroevolution on Trees (Version 2.1.3)

2012
msaR: Multiple Sequence Alignment for R Shiny (Version 0.6.0)

2016
multilaterals: Transitive Index Numbers for Cross-Sections and Panel Data (Version 1.0)

2017
mvMORPH: Multivariate Comparative Tools for Fitting Evolutionary Models to Morphometric Data (Version 1.2.1)

2013
mvSLOUCH: Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses (Version 2.7.6)

2013
nLTT: Calculate the NLTT Statistic (Version 1.4.9)

2015
netdiffuseR: Analysis of Diffusion and Contagion Processes on Networks (Version 1.22.6)

2016
nichevol: Tools for Ecological Niche Evolution Assessment Considering Uncertainty (Version 0.1.20)

2020
nodiv: Compares the Distribution of Sister Clades Through a Phylogeny (Version 1.4.2)

2014
nodeSub: Simulate DNA Alignments Using Node Substitutions (Version 1.2.8)

2021
nosoi: A Forward Agent-Based Transmission Chain Simulator (Version 1.1.2)

2020
numbat: Haplotype-Aware CNV Analysis from scRNA-Seq (Version 1.4.2)

2022
occCite: Querying and Managing Large Biodiversity Occurrence Datasets (Version 0.5.9)

2020
ontophylo: Ontology-Informed Phylogenetic Comparative Analyses (Version 1.1.3)

2023
oppr: Optimal Project Prioritization (Version 1.0.4)

2019
orthGS: Orthology vs Paralogy Relationships among Glutamine Synthetase from Plants (Version 0.1.5)

2024
ouch: Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses (Version 2.20)

2004
outbreaker2: Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data (Version 1.1.3)

2017
outbreaks: A Collection of Disease Outbreak Data (Version 1.9.0)

2016
paco: Procrustes Application to Cophylogenetic Analysis (Version 0.4.2)

2015
palaeoverse: Prepare and Explore Data for Palaeobiological Analyses (Version 1.4.0)

2022
paleoDiv: Extracting and Visualizing Paleobiodiversity (Version 0.4.0)

2024
paleobuddy: Simulating Diversification Dynamics (Version 1.0.0)

2021
paleotree: Paleontological and Phylogenetic Analyses of Evolution (Version 3.4.7)

2012
pcmabc: Approximate Bayesian Computations for Phylogenetic Comparative Methods (Version 1.1.3)

2018
pctax: Professional Comprehensive Omics Data Analysis (Version 0.1.1)

2024
pegas: Population and Evolutionary Genetics Analysis System (Version 1.3)

2009
perspectev: Permutation of Species During Turnover Events (Version 1.1)

2015
pez: Phylogenetics for the Environmental Sciences (Version 1.2-4)

2014
phangorn: Phylogenetic Reconstruction and Analysis (Version 2.12.1)

2008
phyclust: Phylogenetic Clustering (Phyloclustering) (Version 0.1-34)

2010
phyext2: An Extension (for Package 'SigTree') of Some of the Classes in Package 'phylobase' (Version 0.0.4)

2015
phylepic: Combined Visualisation of Phylogenetic and Epidemiological Data (Version 0.2.0)

2024
phyloTop: Calculating Topological Properties of Phylogenies (Version 2.1.2)

2013
phylobase: Base Package for Phylogenetic Structures and Comparative Data (Version 0.8.12)

2009
phylocanvas: Interactive Phylogenetic Trees Using the 'Phylocanvas' JavaScript Library (Version 0.1.3)

2017
phyloclim: Integrating Phylogenetics and Climatic Niche Modeling (Version 0.9.5)

2009
phylocomr: Interface to 'Phylocom' (Version 0.3.4)

2018
phylogram: Dendrograms for Evolutionary Analysis (Version 2.1.0)

2017
phylolm: Phylogenetic Linear Regression (Version 2.6.5)

2013
phylopairs: Comparative Analyses of Lineage-Pair Traits (Version 0.1.0)

2024
phylopath: Perform Phylogenetic Path Analysis (Version 1.3.0)

2016
phyloraster: Evolutionary Diversity Metrics for Raster Data (Version 2.1.0)

2023
phyloregion: Biogeographic Regionalization and Macroecology (Version 1.0.8)

2020
phylosem: Phylogenetic Structural Equation Model (Version 1.1.4)

2023
phylosignal: Exploring the Phylogenetic Signal in Continuous Traits (Version 1.3.1)

2015
phylotate: Phylogenies with Annotations (Version 1.3)

2017
phylotools: Phylogenetic Tools for Eco-Phylogenetics (Version 0.2.2)

2010
phylter: Detect and Remove Outliers in Phylogenomics Datasets (Version 0.9.11)

2023
phyr: Model Based Phylogenetic Analysis (Version 1.1.0)

2019
phytools: Phylogenetic Tools for Comparative Biology (and Other Things) (Version 2.3-0)

2011
picante: Integrating Phylogenies and Ecology (Version 1.8.2)

2008
plotbb: Grammar of Graphics for 'base' Plot (Version 0.0.6)

2021
polysat: Tools for Polyploid Microsatellite Analysis (Version 1.7-7)

2010
pooledpeaks: Genetic Analysis of Pooled Samples (Version 1.0.6)

2024
poolfstat: Computing f-Statistics and Building Admixture Graphs Based on Allele Count or Pool-Seq Read Count Data (Version 2.2.0)

2018
popkin: Estimate Kinship and FST under Arbitrary Population Structure (Version 1.3.23)

2018
poppr: Genetic Analysis of Populations with Mixed Reproduction (Version 2.9.6)

2013
poweRbal: Phylogenetic Tree Models and the Power of Tree Shape Statistics (Version 0.0.1.1)

2024
ppgm: PaleoPhyloGeographic Modeling of Climate Niches and Species Distributions (Version 1.0.3)

2024
primerTree: Visually Assessing the Specificity and Informativeness of Primer Pairs (Version 1.0.6)

2013
prioritizr: Systematic Conservation Prioritization in R (Version 8.0.4)

2016
quiddich: QUick IDentification of DIagnostic CHaracters (Version 1.0.0)

2019
rKOMICS: Minicircle Sequence Classes (MSC) Analyses (Version 1.3)

2021
rapidphylo: Rapidly Estimates Phylogeny from Large Allele Frequency Data Using Root Distances Method (Version 0.1.2)

2022
ratematrix: Bayesian Estimation of the Evolutionary Rate Matrix (Version 1.2.4)

2018
rbiom: Read/Write, Transform, and Summarize 'BIOM' Data (Version 1.0.3)

2020
rdiversity: Measurement and Partitioning of Similarity-Sensitive Biodiversity (Version 2.2.0)

2017
recluster: Ordination Methods for the Analysis of Beta-Diversity Indices (Version 2.9)

2013
rehh: Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests (Version 3.2.2)

2012
restez: Create and Query a Local Copy of 'GenBank' in R (Version 2.1.4)

2018
rhierbaps: Clustering Genetic Sequence Data Using the HierBAPS Algorithm (Version 1.1.4)

2018
rncl: An Interface to the Nexus Class Library (Version 0.8.7)

2014
rotl: Interface to the 'Open Tree of Life' API (Version 3.1.0)

2015
rphylopic: Get Silhouettes of Organisms from PhyloPic (Version 1.5.0)

2018
rr2: R2s for Regression Models (Version 1.1.1)

2018
rrnni: Manipulate with RNNI Tree Space (Version 0.1.1)

2022
rwty: R We There Yet? Visualizing MCMC Convergence in Phylogenetics (Version 1.0.2)

2016
sand: Statistical Analysis of Network Data with R, 2nd Edition (Version 2.0.0)

2014
scistreer: Maximum-Likelihood Perfect Phylogeny Inference at Scale (Version 1.2.0)

2022
scrm: Simulating the Evolution of Biological Sequences (Version 1.7.5)

2014
secsse: Several Examined and Concealed States-Dependent Speciation and Extinction (Version 3.1.0)

2019
sensiPhy: Sensitivity Analysis for Comparative Methods (Version 0.8.5)

2016
sharpshootR: A Soil Survey Toolkit (Version 2.3.2)

2014
shazam: Immunoglobulin Somatic Hypermutation Analysis (Version 1.2.0)

2016
shinyTempSignal: Explore Temporal and Other Phylogenetic Signals (Version 0.0.8)

2022
shinyWGD: 'Shiny' Application for Whole Genome Duplication Analysis (Version 1.0.0)

0
shipunov: Miscellaneous Functions from Alexey Shipunov (Version 1.17.1)

2019
sidier: Substitution and Indel Distances to Infer Evolutionary Relationships (Version 4.1.0)

2013
slendr: A Simulation Framework for Spatiotemporal Population Genetics (Version 0.9.1)

2022
slouch: Stochastic Linear Ornstein-Uhlenbeck Comparative Hypotheses (Version 2.1.5)

2018
spANOVA: Analysis of Field Trials with Geostatistics & Spatial AR Models (Version 0.99.4)

2019
spider: Species Identity and Evolution in R (Version 1.5.0)

2011
spiralize: Visualize Data on Spirals (Version 1.1.0)

2021
strap: Stratigraphic Tree Analysis for Palaeontology (Version 1.6-1)

2014
stylo: Stylometric Multivariate Analyses (Version 0.7.5)

2013
supportR: Support Functions for Wrangling and Visualization (Version 1.4.0)

2023
surface: Fitting Hansen Models to Investigate Convergent Evolution (Version 0.6)

2013
symmoments: Symbolic Central and Noncentral Moments of the Multivariate Normal Distribution (Version 1.2.1)

2010
tapnet: Trait Matching and Abundance for Predicting Bipartite Networks (Version 0.3)

2021
taxlist: Handling Taxonomic Lists (Version 0.3.0)

2017
tbea: Pre- And Post-Processing in Bayesian Evolutionary Analyses (Version 1.5.0)

2024
tidygraph: A Tidy API for Graph Manipulation (Version 1.3.1)

2017
tidysq: Tidy Processing and Analysis of Biological Sequences (Version 1.2.2)

2021
tidytree: A Tidy Tool for Phylogenetic Tree Data Manipulation (Version 0.4.6)

2017
tracerer: Tracer from R (Version 2.2.3)

2018
treats: Trees and Traits Simulations (Version 1.0)

2023
treeDA: Tree-Based Discriminant Analysis (Version 0.0.5)

2017
treebalance: Computation of Tree (Im)Balance Indices (Version 1.2.0)

2021
treebase: Discovery, Access and Manipulation of 'TreeBASE' Phylogenies (Version 0.1.5)

2011
treedater: Fast Molecular Clock Dating of Phylogenetic Trees with Rate Variation (Version 0.5.0)

2018
treenomial: Comparison of Trees using a Tree Defining Polynomial (Version 1.1.4)

2019
treesliceR: To Slice Phylogenetic Trees and Infer Evolutionary Patterns Over Time (Version 1.0.2)

2023
treespace: Statistical Exploration of Landscapes of Phylogenetic Trees (Version 1.1.4.3)

2017
treestartr: Generate Starting Trees for Combined Molecular, Morphological and Stratigraphic Data (Version 0.1.0)

2019
treestats: Phylogenetic Tree Statistics (Version 1.70.5)

2024
treestructure: Detect Population Structure Within Phylogenetic Trees (Version 0.1.0)

2020
vcfR: Manipulate and Visualize VCF Data (Version 1.15.0)

2016
vhica: Vertical and Horizontal Inheritance Consistence Analysis (Version 0.2.8)

2016
warbleR: Streamline Bioacoustic Analysis (Version 1.1.32)

2015
windex: Analysing Convergent Evolution using the Wheatsheaf Index (Version 2.0.8)

2014
yatah: Yet Another TAxonomy Handler (Version 1.0.0)

2019

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