Ecosyste.ms: Packages

An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.

Top 5.6% on cran.r-project.org
Top 1.5% downloads on cran.r-project.org
Top 0.3% dependent packages on cran.r-project.org
Top 0.4% dependent repos on cran.r-project.org
Top 5.9% forks on cran.r-project.org

cran.r-project.org : ape

Analyses of Phylogenetics and Evolution

Registry - Source - Documentation - JSON
purl: pkg:cran/ape
License: GPL-2.0+
Latest release: about 2 months ago
First release: almost 22 years ago
Dependent packages: 394
Dependent repositories: 965
Downloads: 114,956 last month
Stars: 45 on GitHub
Forks: 12 on GitHub
Docker dependents: 325
Docker downloads: 894,238
Total Commits: 153
Committers: 11
Average commits per author: 13.909
Development Distribution Score (DDS): 0.471
More commit stats: commits.ecosyste.ms
See more repository details: repos.ecosyste.ms
Last synced: 20 days ago

genBaRcode 1.2.7
Analysis and Visualization Tools for Genetic Barcode Data
9 versions - Latest release: 6 months ago - 314 downloads last month - 1 maintainer
mvMORPH 1.1.9
Multivariate Comparative Tools for Fitting Evolutionary Models to Morphometric Data
20 versions - Latest release: 6 months ago - 5 dependent packages - 7 dependent repositories - 713 downloads last month - 16 stars on GitHub - 1 maintainer
Top 6.6% on cran.r-project.org
vcfR 1.15.0
Manipulate and Visualize VCF Data
16 versions - Latest release: 6 months ago - 25 dependent packages - 55 dependent repositories - 7.22 thousand downloads last month - 233 stars on GitHub - 1 maintainer
evolqg 0.3-4
Evolutionary Quantitative Genetics
17 versions - Latest release: 6 months ago - 2 dependent packages - 2 dependent repositories - 400 downloads last month - 9 stars on GitHub - 1 maintainer
RevGadgets 1.2.1
Visualization and Post-Processing of 'RevBayes' Analyses
5 versions - Latest release: 6 months ago - 1 dependent package - 1 dependent repositories - 277 downloads last month - 13 stars on GitHub - 1 maintainer
Rogue 2.1.6
Identify Rogue Taxa in Sets of Phylogenetic Trees
9 versions - Latest release: 6 months ago - 2 dependent packages - 3 dependent repositories - 420 downloads last month - 2 stars on GitHub - 1 maintainer
cauphy 1.0.2
Trait Evolution on Phylogenies Using the Cauchy Process
3 versions - Latest release: 6 months ago - 204 downloads last month - 1 stars on GitHub - 1 maintainer
jackalope 1.1.5
A Swift, Versatile Phylogenomic and High-Throughput Sequencing Simulator
11 versions - Latest release: 6 months ago - 803 downloads last month - 8 stars on GitHub - 1 maintainer
Top 3.9% on cran.r-project.org
FD 1.0-12.3
Measuring Functional Diversity (FD) from Multiple Traits, and Other Tools for Functional Ecology
10 versions - Latest release: 6 months ago - 14 dependent packages - 28 dependent repositories - 3.98 thousand downloads last month - 1 maintainer
JNplots 0.1.1
Visualize Outputs from the 'Johnson-Neyman' Technique
2 versions - Latest release: 6 months ago - 197 downloads last month - 0 stars on GitHub - 1 maintainer
mvSLOUCH 2.7.6
Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses
41 versions - Latest release: 7 months ago - 3 dependent packages - 2 dependent repositories - 668 downloads last month - 1 maintainer
itol.toolkit 1.1.7
Helper Functions for 'Interactive Tree Of Life'
4 versions - Latest release: 7 months ago - 1 dependent repositories - 332 downloads last month - 1 maintainer
dartR.base 0.65
Analysing 'SNP' and 'Silicodart' Data - Basic Functions
2 versions - Latest release: 7 months ago - 2 dependent packages - 1 dependent repositories - 676 downloads last month - 29 stars on GitHub - 1 maintainer
SoilTaxonomy 0.2.4
A System of Soil Classification for Making and Interpreting Soil Surveys
8 versions - Latest release: 7 months ago - 1 dependent package - 1 dependent repositories - 349 downloads last month - 14 stars on GitHub - 1 maintainer
nodeSub 1.2.8
Simulate DNA Alignments Using Node Substitutions
7 versions - Latest release: 7 months ago - 2 dependent packages - 2 dependent repositories - 265 downloads last month - 1 stars on GitHub - 1 maintainer
Momocs 1.4.1
Morphometrics using R
19 versions - Latest release: 7 months ago - 1 dependent package - 3 dependent repositories - 827 downloads last month - 49 stars on GitHub - 1 maintainer
Top 5.2% on cran.r-project.org
data.tree 1.1.0
General Purpose Hierarchical Data Structure
18 versions - Latest release: 7 months ago - 61 dependent packages - 137 dependent repositories - 12.3 thousand downloads last month - 206 stars on GitHub - 1 maintainer
ecotraj 0.1.1
Ecological Trajectory Analysis
3 versions - Latest release: 7 months ago - 1 dependent package - 1 dependent repositories - 677 downloads last month - 3 stars on GitHub - 1 maintainer
MSCquartets 1.3.2
Analyzing Gene Tree Quartets under the Multi-Species Coalescent
7 versions - Latest release: 7 months ago - 362 downloads last month - 1 maintainer
restez 2.1.4
Create and Query a Local Copy of 'GenBank' in R
4 versions - Latest release: 7 months ago - 1 dependent repositories - 265 downloads last month - 25 stars on GitHub - 1 maintainer
TreeDist 2.7.0
Calculate and Map Distances Between Phylogenetic Trees
19 versions - Latest release: 7 months ago - 3 dependent packages - 5 dependent repositories - 25 stars on GitHub - 1 maintainer
missSBM 1.0.4
Handling Missing Data in Stochastic Block Models
8 versions - Latest release: 7 months ago - 1 dependent package - 1 dependent repositories - 323 downloads last month - 12 stars on GitHub - 1 maintainer
CRABS 1.2.0
Congruent Rate Analyses in Birth-Death Scenarios
2 versions - Latest release: 7 months ago - 230 downloads last month - 7 stars on GitHub - 1 maintainer
DAISIE 4.4.1
Dynamical Assembly of Islands by Speciation, Immigration and Extinction
11 versions - Latest release: 8 months ago - 3 dependent packages - 12 dependent repositories - 311 downloads last month - 9 stars on GitHub - 1 maintainer
dynamicSDM 1.3.3
Species Distribution and Abundance Modelling at High Spatio-Temporal Resolution
7 versions - Latest release: 8 months ago - 314 downloads last month - 4 stars on GitHub - 1 maintainer
Top 10.0% on cran.r-project.org
adespatial 0.3-23 removed
Multivariate Multiscale Spatial Analysis
25 versions - Latest release: 8 months ago - 5 dependent packages - 12 dependent repositories - 2.17 thousand downloads last month - 29 stars on GitHub - 1 maintainer
Top 7.9% on cran.r-project.org
ecospat 4.0.0
Spatial Ecology Miscellaneous Methods
17 versions - Latest release: 8 months ago - 8 dependent packages - 12 dependent repositories - 2.16 thousand downloads last month - 1 maintainer
phylosignal 1.3.1
Exploring the Phylogenetic Signal in Continuous Traits
5 versions - Latest release: 8 months ago - 3 dependent packages - 1 dependent repositories - 493 downloads last month - 1 maintainer
divraster 1.0.4
Diversity Metrics Calculations for Rasterized Data
3 versions - Latest release: 8 months ago - 245 downloads last month - 8 stars on GitHub - 1 maintainer
beastier 2.4.12
Call 'BEAST2'
16 versions - Latest release: 8 months ago - 5 dependent packages - 10 dependent repositories - 533 downloads last month - 1 maintainer
pirouette 1.6.9 removed
Create a Bayesian Posterior from a Phylogeny
6 versions - Latest release: 8 months ago - 17 dependent repositories - 476 downloads last month - 3 stars on GitHub - 1 maintainer
Top 8.3% on cran.r-project.org
adephylo 1.1-16
Exploratory Analyses for the Phylogenetic Comparative Method
13 versions - Latest release: 8 months ago - 8 dependent packages - 18 dependent repositories - 7 thousand downloads last month - 1 maintainer
pmc 1.0.6
Phylogenetic Monte Carlo
11 versions - Latest release: 8 months ago - 1 dependent package - 479 downloads last month - 2 stars on GitHub - 1 maintainer
shazam 1.2.0
Immunoglobulin Somatic Hypermutation Analysis
21 versions - Latest release: 8 months ago - 3 dependent packages - 2 dependent repositories - 737 downloads last month - 1 maintainer
alakazam 1.3.0
Immunoglobulin Clonal Lineage and Diversity Analysis
18 versions - Latest release: 8 months ago - 8 dependent packages - 7 dependent repositories - 1.5 thousand downloads last month - 1 maintainer
mcbette 1.15.2 removed
Model Comparison Using 'babette'
5 versions - Latest release: 8 months ago - 1 dependent package - 1 dependent repositories - 452 downloads last month - 7 stars on GitHub - 1 maintainer
babette 2.3.3 removed
Control 'BEAST2'
8 versions - Latest release: 8 months ago - 3 dependent packages - 4 dependent repositories - 599 downloads last month - 1 maintainer
tracerer 2.2.3
Tracer from R
6 versions - Latest release: 8 months ago - 5 dependent packages - 10 dependent repositories - 301 downloads last month - 1 maintainer
Top 5.3% on cran.r-project.org
caper 1.0.3
Comparative Analyses of Phylogenetics and Evolution in R
8 versions - Latest release: 8 months ago - 10 dependent packages - 26 dependent repositories - 1.84 thousand downloads last month - 1 maintainer
Top 1.5% on cran.r-project.org
clue 0.3-65
Cluster Ensembles
77 versions - Latest release: 9 months ago - 50 dependent packages - 105 dependent repositories - 42.1 thousand downloads last month - 1 maintainer
markophylo 1.0.9 removed
Markov Chain Models for Phylogenetic Trees
8 versions - Latest release: 9 months ago - 400 downloads last month - 1 maintainer
indelmiss 1.0.10 removed
Insertion Deletion Analysis While Accounting for Possible Missing Data
4 versions - Latest release: 9 months ago - 239 downloads last month - 1 maintainer
asnipe 1.1.17
Animal Social Network Inference and Permutations for Ecologists
21 versions - Latest release: 9 months ago - 2 dependent packages - 5 dependent repositories - 894 downloads last month - 1 maintainer
DCLEAR 1.0.13
Distance Based Cell Lineage Reconstruction
5 versions - Latest release: 9 months ago - 1 dependent repositories - 247 downloads last month - 6 stars on GitHub - 1 maintainer
GUniFrac 1.8
Generalized UniFrac Distances, Distance-Based Multivariate Methods and Feature-Based Univariate M...
9 versions - Latest release: 9 months ago - 6 dependent packages - 17 dependent repositories - 1.72 thousand downloads last month - 1 maintainer
mecoturn 0.3.0
Decipher Microbial Turnover along a Gradient
3 versions - Latest release: 9 months ago - 312 downloads last month - 1 stars on GitHub - 1 maintainer
Top 9.3% on cran.r-project.org
HSAUR2 1.1-20
A Handbook of Statistical Analyses Using R (2nd Edition)
28 versions - Latest release: 9 months ago - 8 dependent packages - 19 dependent repositories - 2.5 thousand downloads last month - 1 maintainer
aphylo 0.3-3 removed
Statistical Inference and Prediction of Annotations in Phylogenetic Trees
4 versions - Latest release: 9 months ago - 278 downloads last month - 6 stars on GitHub - 1 maintainer
phyclust 0.1-34
Phylogenetic Clustering (Phyloclustering)
33 versions - Latest release: 9 months ago - 6 dependent packages - 21 dependent repositories - 1.91 thousand downloads last month - 9 stars on GitHub - 1 maintainer
poolfstat 2.2.0
Computing f-Statistics and Building Admixture Graphs Based on Allele Count or Pool-Seq Read Count...
9 versions - Latest release: 9 months ago - 415 downloads last month - 1 maintainer
netdiffuseR 1.22.6
Analysis of Diffusion and Contagion Processes on Networks
15 versions - Latest release: 9 months ago - 4 dependent repositories - 561 downloads last month - 83 stars on GitHub - 1 maintainer
rrnni 0.1.1
Manipulate with RNNI Tree Space
2 versions - Latest release: 9 months ago - 209 downloads last month - 1 stars on GitHub - 1 maintainer
phylter 0.9.11
Detect and Remove Outliers in Phylogenomics Datasets
3 versions - Latest release: 10 months ago - 270 downloads last month - 8 stars on GitHub - 1 maintainer
rr2 1.1.1
R2s for Regression Models
5 versions - Latest release: 10 months ago - 2 dependent packages - 5 dependent repositories - 3.37 thousand downloads last month - 16 stars on GitHub - 1 maintainer
nodiv 1.4.2
Compares the Distribution of Sister Clades Through a Phylogeny
21 versions - Latest release: 10 months ago - 370 downloads last month - 2 stars on GitHub - 1 maintainer
nLTT 1.4.9
Calculate the NLTT Statistic
13 versions - Latest release: 10 months ago - 5 dependent packages - 12 dependent repositories - 404 downloads last month - 6 stars on GitHub - 1 maintainer
gamclass 0.62.5
Functions and Data for a Course on Modern Regression and Classification
8 versions - Latest release: 10 months ago - 1 dependent repositories - 368 downloads last month - 1 maintainer
hillR 0.5.2
Diversity Through Hill Numbers
4 versions - Latest release: 10 months ago - 1 dependent package - 3 dependent repositories - 665 downloads last month - 29 stars on GitHub - 1 maintainer
TreeTools 1.10.0
Create, Modify and Analyse Phylogenetic Trees
26 versions - Latest release: 10 months ago - 7 dependent packages - 13 dependent repositories - 1.04 thousand downloads last month - 15 stars on GitHub - 1 maintainer
chemodiv 0.3.0
Analysing Chemodiversity of Phytochemical Data
4 versions - Latest release: 10 months ago - 323 downloads last month - 2 stars on GitHub - 1 maintainer
phyloregion 1.0.8
Biogeographic Regionalization and Macroecology
4 versions - Latest release: 10 months ago - 2 dependent packages - 3 dependent repositories - 401 downloads last month - 17 stars on GitHub - 1 maintainer
Top 9.8% on cran.r-project.org
prioritizr 8.0.3
Systematic Conservation Prioritization in R
21 versions - Latest release: 10 months ago - 1 dependent package - 4 dependent repositories - 1.21 thousand downloads last month - 118 stars on GitHub - 1 maintainer
DDD 5.2.2
Diversity-Dependent Diversification
40 versions - Latest release: 11 months ago - 9 dependent packages - 14 dependent repositories - 828 downloads last month - 1 maintainer
Rarefy 1.1.1 removed
Rarefaction Methods
3 versions - Latest release: 11 months ago - 457 downloads last month - 1 maintainer
convevol 2.0.1
Analysis of Convergent Evolution
8 versions - Latest release: 11 months ago - 382 downloads last month - 1 maintainer
haplotypes 1.1.3
Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony
6 versions - Latest release: 11 months ago - 1 dependent package - 1 dependent repositories - 415 downloads last month - 1 maintainer
rKOMICS 1.3
Minicircle Sequence Classes (MSC) Analyses
4 versions - Latest release: 11 months ago - 229 downloads last month - 1 maintainer
EpiModel 2.4.0
Mathematical Modeling of Infectious Disease Dynamics
39 versions - Latest release: 12 months ago - 2 dependent packages - 10 dependent repositories - 1.07 thousand downloads last month - 1 maintainer
Top 9.3% on cran.r-project.org
ggimage 0.3.3
Use Image in 'ggplot2'
25 versions - Latest release: 12 months ago - 16 dependent packages - 45 dependent repositories - 15.4 thousand downloads last month - 1 maintainer
datelife 0.6.8
Scientific Data on Time of Lineage Divergence for Your Taxa
6 versions - Latest release: 12 months ago - 3 dependent repositories - 370 downloads last month - 11 stars on GitHub - 1 maintainer
rotl 3.1.0
Interface to the 'Open Tree of Life' API
15 versions - Latest release: 12 months ago - 4 dependent packages - 15 dependent repositories - 3.78 thousand downloads last month - 39 stars on GitHub - 1 maintainer
scistreer 1.2.0
Maximum-Likelihood Perfect Phylogeny Inference at Scale
4 versions - Latest release: 12 months ago - 1 dependent package - 359 downloads last month - 5 stars on GitHub - 1 maintainer
dartR 2.9.7
Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment...
17 versions - Latest release: 12 months ago - 1 dependent package - 1 dependent repositories - 1.49 thousand downloads last month - 29 stars on GitHub - 1 maintainer
SPARTAAS 1.2.1
Statistical Pattern Recognition and daTing using Archaeological Artefacts assemblageS
4 versions - Latest release: 12 months ago - 205 downloads last month - 1 maintainer
RRphylo 2.8.0
Phylogenetic Ridge Regression Methods for Comparative Studies
14 versions - Latest release: about 1 year ago - 1 dependent repositories - 496 downloads last month - 1 maintainer
TiPS 1.2.3
Trajectories and Phylogenies Simulator
7 versions - Latest release: about 1 year ago - 1 dependent repositories - 243 downloads last month - 1 maintainer
mmodely 0.2.5
Modeling Multivariate Origins Determinants - Evolutionary Lineages in Ecology
3 versions - Latest release: about 1 year ago - 239 downloads last month - 1 maintainer
safedata 1.1.3 removed
Interface to Data from the SAFE Project
9 versions - Latest release: about 1 year ago - 301 downloads last month - 3 stars on GitHub - 1 maintainer
canaper 1.0.1
Categorical Analysis of Neo- And Paleo-Endemism
2 versions - Latest release: about 1 year ago - 240 downloads last month - 6 stars on GitHub - 1 maintainer
sandwichr 1.0.4 removed
Spatial Prediction Based on Spatial Stratified Heterogeneity
5 versions - Latest release: about 1 year ago - 196 downloads last month - 2 stars on GitHub - 1 maintainer
CALANGO 1.0.16
Comparative Analysis with Annotation-Based Genomic Components
6 versions - Latest release: about 1 year ago - 319 downloads last month - 0 stars on GitHub - 1 maintainer
ouch 2.19
Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses
29 versions - Latest release: about 1 year ago - 5 dependent packages - 10 dependent repositories - 694 downloads last month - 15 stars on GitHub - 1 maintainer
phylocomr 0.3.4 removed
Interface to 'Phylocom'
8 versions - Latest release: about 1 year ago - 2 dependent packages - 5 dependent repositories - 516 downloads last month - 14 stars on GitHub - 1 maintainer
Top 6.5% on cran.r-project.org
HSAUR3 1.0-14
A Handbook of Statistical Analyses Using R (3rd Edition)
15 versions - Latest release: about 1 year ago - 11 dependent packages - 16 dependent repositories - 4.68 thousand downloads last month - 1 maintainer
SiPhyNetwork 1.1.0
A Phylogenetic Simulator for Reticulate Evolution
3 versions - Latest release: about 1 year ago - 656 downloads last month - 1 maintainer
Top 8.6% on cran.r-project.org
geiger 2.0.11
Analysis of Evolutionary Diversification
28 versions - Latest release: about 1 year ago - 43 dependent packages - 86 dependent repositories - 5.06 thousand downloads last month - 1 maintainer
Top 4.5% on cran.r-project.org
dendextend 1.17.1
Extending 'dendrogram' Functionality in R
29 versions - Latest release: about 1 year ago - 71 dependent packages - 188 dependent repositories - 70.5 thousand downloads last month - 147 stars on GitHub - 1 maintainer
fido 1.0.4
Bayesian Multinomial Logistic Normal Regression
6 versions - Latest release: about 1 year ago - 1 dependent repositories - 297 downloads last month - 19 stars on GitHub - 1 maintainer
taxlist 0.2.4
Handling Taxonomic Lists
15 versions - Latest release: about 1 year ago - 1 dependent package - 6 dependent repositories - 368 downloads last month - 1 maintainer
nichevol 0.1.20 removed
Tools for Ecological Niche Evolution Assessment Considering Uncertainty
2 versions - Latest release: about 1 year ago - 143 downloads last month - 14 stars on GitHub - 1 maintainer
FuncDiv 1.0.0
Compute Contributional Diversity Metrics
1 version - Latest release: about 1 year ago - 248 downloads last month - 1 maintainer
vhica 0.2.8
Vertical and Horizontal Inheritance Consistence Analysis
3 versions - Latest release: about 1 year ago - 197 downloads last month - 1 maintainer
Sysrecon 0.1.3
Systematical Metabolic Reconstruction
4 versions - Latest release: over 1 year ago - 233 downloads last month - 0 stars on GitHub - 1 maintainer
autoGO 0.9.1
Auto-GO: Reproducible, Robust and High Quality Ontology Enrichment Visualizations
2 versions - Latest release: over 1 year ago - 271 downloads last month - 2 stars on GitHub - 1 maintainer
ggmuller 0.5.6
Create Muller Plots of Evolutionary Dynamics
9 versions - Latest release: over 1 year ago - 2 dependent repositories - 367 downloads last month - 1 maintainer
hisse 2.1.11
Hidden State Speciation and Extinction
34 versions - Latest release: over 1 year ago - 1 dependent package - 1 dependent repositories - 660 downloads last month - 1 maintainer
Top 1.6% on cran.r-project.org
ade4 1.7-22
Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences
47 versions - Latest release: over 1 year ago - 96 dependent packages - 202 dependent repositories - 39.4 thousand downloads last month - 1 maintainer
shipunov 1.17.1
Miscellaneous Functions from Alexey Shipunov
19 versions - Latest release: over 1 year ago - 436 downloads last month - 1 maintainer
RNeXML 2.4.11
Semantically Rich I/O for the 'NeXML' Format
28 versions - Latest release: over 1 year ago - 2 dependent packages - 7 dependent repositories - 3.75 thousand downloads last month - 12 stars on GitHub - 1 maintainer
rapidphylo 0.1.2
Rapidly Estimates Phylogeny from Large Allele Frequency Data Using Root Distances Method
3 versions - Latest release: over 1 year ago - 155 downloads last month - 0 stars on GitHub - 1 maintainer