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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