vegan - Community Ecology Package
Ordination methods, diversity analysis and other functions for community and vegetation ecologists.
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ecological-modellingecologyordinationopenblasfortran
19.92 score 549 stars 460 dependents 34k scripts 135k downloads
brms - Bayesian Regression Models using 'Stan'
Fit Bayesian generalized (non-)linear multivariate multilevel models using 'Stan' for full Bayesian inference. A wide range of distributions and link functions are supported, allowing users to fit -- among others -- linear, robust linear, count data, survival, response times, ordinal, zero-inflated, hurdle, and even self-defined mixture models all in a multilevel context. Further modeling options include both theory-driven and data-driven non-linear terms, auto-correlation structures, censoring and truncation, meta-analytic standard errors, and quite a few more. In addition, all parameters of the response distribution can be predicted in order to perform distributional regression. Prior specifications are flexible and explicitly encourage users to apply prior distributions that actually reflect their prior knowledge. Models can easily be evaluated and compared using several methods assessing posterior or prior predictions. References: Bürkner (2017) <doi:10.18637/jss.v080.i01>; Bürkner (2018) <doi:10.32614/RJ-2018-017>; Bürkner (2021) <doi:10.18637/jss.v100.i05>; Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>.
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bayesian-inferencebrmsmultilevel-modelsstanstatistical-models
17.22 score 1.4k stars 46 dependents 19k scripts 44k downloads
phangorn - Phylogenetic Reconstruction and Analysis
Allows for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation (Schliep 2011). Offers methods for tree comparison, model selection and visualization of phylogenetic networks as described in Schliep et al. (2017).
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softwaretechnologyqualitycontrolphylogenetic-analysisphylogeneticsopenblascpp
17.06 score 216 stars 139 dependents 4.0k scripts 25k downloads
rotl - Interface to the 'Open Tree of Life' API
An interface to the 'Open Tree of Life' API to retrieve phylogenetic trees, information about studies used to assemble the synthetic tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The 'Open Tree of Life' aims at assembling a comprehensive phylogenetic tree for all named species.
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metadataropensciphylogeneticsindependant-contrastsbiodiversitypeer-reviewedphylogenytaxonomy
12.00 score 46 stars 19 dependents 482 scripts 5.2k downloadspicante - Integrating Phylogenies and Ecology
Functions for phylocom integration, community analyses, null-models, traits and evolution. Implements numerous ecophylogenetic approaches including measures of community phylogenetic and trait diversity, phylogenetic signal, estimation of trait values for unobserved taxa, null models for community and phylogeny randomizations, and utility functions for data input/output and phylogeny plotting. A full description of package functionality and methods are provided by Kembel et al. (2010) <doi:10.1093/bioinformatics/btq166>.
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11.99 score 41 stars 15 dependents 1.9k scripts 8.0k downloadsTreeTools - Create, Modify and Analyse Phylogenetic Trees
Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; tree rearrangement; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of split support; plotting the position of rogue taxa (Klopfstein & Spasojevic 2019) <doi:10.1371/journal.pone.0212942>; calculation of ancestor-descendant relationships, of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>, and of tree balance (Mir et al. 2013, Lemant et al. 2022) <doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>; artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>; import and export of trees from Newick, Nexus (Maddison et al. 1997) <doi:10.1093/sysbio/46.4.590>, and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats; and analysis of splits and cladistic information.
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cladisticsevolutionary-biologyphylogenetic-treesphylogeneticscpp
11.72 score 24 stars 17 dependents 620 scripts 3.6k downloadsTreeDist - Calculate and Map Distances Between Phylogenetic Trees
Implements measures of tree similarity, including information-based generalized Robinson-Foulds distances (Phylogenetic Information Distance, Clustering Information Distance, Matching Split Information Distance; Smith 2020) <doi:10.1093/bioinformatics/btaa614>; Jaccard-Robinson-Foulds distances (Bocker et al. 2013) <doi:10.1007/978-3-642-40453-5_13>, including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>; the Matching Split Distance (Bogdanowicz & Giaro 2012) <doi:10.1109/TCBB.2011.48>; the Hierarchical Mutual Information (Perotti et al. 2015) <doi:10.1103/PhysRevE.92.062825>; Maximum Agreement Subtree distances; the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the Nearest Neighbour Interchange (NNI) distance, approximated per Li et al. (1996) <doi:10.1007/3-540-61332-3_168>. Includes tools for visualizing mappings of tree space (Smith 2022) <doi:10.1093/sysbio/syab100>, for identifying islands of trees (Silva and Wilkinson 2021) <doi:10.1093/sysbio/syab015>, for calculating the median of sets of trees, and for computing the information content of trees and splits.
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phylogeneticstree-distancebioinformaticscladisticsentropyinformation-theorymutual-informationphylogenetic-treestree-distancestreescppopenmp
11.65 score 40 stars 5 dependents 300 scripts 2.4k downloadsgeiger - Analysis of Evolutionary Diversification
Methods for fitting macroevolutionary models to phylogenetic trees Pennell (2014) <doi:10.1093/bioinformatics/btu181>.
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openblascpp
11.52 score 26 stars 30 dependents 2.8k scripts 10k downloadsphylolm - Phylogenetic Linear Regression
Provides functions for fitting phylogenetic linear models and phylogenetic generalized linear models. The computation uses an algorithm that is linear in the number of tips in the tree. The package also provides functions for simulating continuous or binary traits along the tree. Other tools include functions to test the adequacy of a population tree.
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11.37 score 35 stars 18 dependents 604 scripts 14k downloadstidytree - A Tidy Tool for Phylogenetic Tree Data Manipulation
Phylogenetic trees contain components such as nodes, edges, branches, and associated data. As the core data manipulation tool in the 'ggtree' ecosystem, 'tidytree' provides tools for converting tree objects to tidy data frames and tidy interfaces for manipulating, analyzing, and visualizing tree data.
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phylogenetic-treetidyversetree-data
11.27 score 61 stars 157 dependents 72k downloadsMCMCglmm - MCMC Generalised Linear Mixed Models
Fits Multivariate Generalised Linear Mixed Models (and related models) using Markov chain Monte Carlo techniques (Hadfield 2010 J. Stat. Soft.).
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cpp
11.01 score 5 stars 11 dependents 2.1k scripts 9.0k downloads
deeptime - Plotting Tools for Anyone Working in Deep Time
Extends the functionality of other plotting packages (notably 'ggplot2') to help facilitate the plotting of data over long time intervals, including, but not limited to, geological, evolutionary, and ecological data. The primary goal of 'deeptime' is to enable users to add highly customizable timescales to their visualizations. Other functions are also included to assist with other areas of deep time visualization.
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geologyggplot2paleontologyvisualization
10.95 score 108 stars 4 dependents 449 scripts 948 downloadsgeomorph - Geometric Morphometric Analyses of 2D and 3D Landmark Data
Read and manipulate landmark data, generate shape variables via Procrustes analysis for points, curves and surfaces, perform shape analyses, and provide graphical depictions of shapes and patterns of shape variation.
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10.81 score 92 stars 3 dependents 1.1k scripts 2.6k downloadstaxize - Taxonomic Information from Around the Web
Interacts with a suite of web application programming interfaces (API) for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more. Some of the services supported include 'NCBI E-utilities' (<https://www.ncbi.nlm.nih.gov/books/NBK25501/>), 'Encyclopedia of Life' (<https://eol.org/docs/what-is-eol/data-services>), 'Global Biodiversity Information Facility' (<https://techdocs.gbif.org/en/openapi/>), and many more. Links to the API documentation for other supported services are available in the documentation for their respective functions in this package.
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taxonomybiologynomenclaturejsonapiwebapi-clientidentifiersspeciesnamesapi-wrapperbiodiversitydarwincoredatataxize
10.63 score 303 stars 14 dependents 2 scripts 4.9k downloadsmvMORPH - Multivariate Comparative Tools for Fitting Evolutionary Models to Morphometric Data
Fits multivariate (Brownian Motion, Early Burst, ACDC, Ornstein-Uhlenbeck and Shifts) models of continuous traits evolution on trees and time series. 'mvMORPH' also proposes high-dimensional multivariate comparative tools (linear models using Generalized Least Squares and multivariate tests) based on penalized likelihood and Empirical Bayes approaches. See Clavel et al. (2015) <DOI:10.1111/2041-210X.12420>, Clavel et al. (2019) <DOI:10.1093/sysbio/syy045>, Clavel & Morlon (2020) <DOI:10.1093/sysbio/syaa010>, and Montoya et al. (2026) <DOI:10.1093/sysbio/syag051>.
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openblas
10.18 score 20 stars 3 dependents 254 scripts 1.0k downloadsOUwie - Analysis of Evolutionary Rates in an OU Framework
Estimates rates for continuous character evolution under Brownian motion and Ornstein-Uhlenbeck based Hansen models that allow both the strength of the pull and stochastic motion to vary across selective regimes. Beaulieu et al. (2012).
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9.47 score 11 stars 210 scripts 969 downloadscorHMM - Hidden Markov Models of Character Evolution
Fits hidden Markov models of discrete character evolution which allow different transition rate classes on different portions of a phylogeny. Beaulieu et al (2013) <doi:10.1093/sysbio/syt034>.
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9.25 score 15 stars 2 dependents 560 scripts 2.4k downloadsrncl - An Interface to the Nexus Class Library
An interface to the Nexus Class Library which allows parsing of NEXUS, Newick and other phylogenetic tree file formats. It provides elements of the file that can be used to build phylogenetic objects such as ape's 'phylo' or phylobase's 'phylo4(d)'. This functionality is demonstrated with 'read_newick_phylo()' and 'read_nexus_phylo()'.
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newicknexusphylogeneticstree-parsingcpp
8.86 score 9 stars 37 dependents 46 scripts 10k downloadsRRphylo - Phylogenetic Ridge Regression Methods for Comparative Studies
Functions for phylogenetic analysis (Castiglione et al., 2018 <doi:10.1111/2041-210X.12954>). The functions perform the estimation of phenotypic evolutionary rates, identification of phenotypic evolutionary rate shifts, quantification of direction and size of evolutionary change in multivariate traits, the computation of ontogenetic shape vectors and test for morphological convergence.
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8.56 score 11 stars 3 dependents 102 scripts 788 downloadshisse - Hidden State Speciation and Extinction
Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character sets to test for hidden shifts in trait dependent rates of diversification. Beaulieu and O'Meara (2016) <doi:10.1093/sysbio/syw022>.
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8.55 score 7 stars 200 scripts 780 downloadsdispRity - Measuring Disparity
A modular package for measuring disparity (multidimensional space occupancy). Disparity can be calculated from any matrix defining a multidimensional space. The package provides a set of implemented metrics to measure properties of the space and allows users to provide and test their own metrics. The package also provides functions for looking at disparity in a serial way (e.g. disparity through time) or per groups as well as visualising the results. Finally, this package provides several statistical tests for disparity analysis.
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disparityecologymultidimensionalitypalaeobiology
8.43 score 29 stars 1 dependents 285 scripts 789 downloadsQuartet - Comparison of Phylogenetic Trees Using Quartet and Split Measures
Calculates the number of four-taxon subtrees consistent with a pair of cladograms, calculating the symmetric quartet distance of Bandelt & Dress (1986), Reconstructing the shape of a tree from observed dissimilarity data, Advances in Applied Mathematics <doi:10.1016/0196-8858(86)90038-2>, using the tqDist algorithm of Sand et al. (2014), tqDist: a library for computing the quartet and triplet distances between binary or general trees, Bioinformatics <doi:10.1093/bioinformatics/btu157> for pairs of binary trees; calculating the rooted triplet distance using the CPDT algorithm of Jansson & Rajaby (2017), A more practical algorithm for the rooted triplet distance, Journal of Computational Biology <doi:10.1089/cmb.2016.0185>.
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bioinformaticscomparisonphylogenetic-treesphylogeneticsquartetquartet-distanceresearch-tooltreecppopenmp
8.41 score 18 stars 65 scripts 998 downloadsbeautier - 'BEAUti' from R
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAUti 2' (which is part of 'BEAST2') is a GUI tool that allows users to specify the many possible setups and generates the XML file 'BEAST2' needs to run. This package provides a way to create 'BEAST2' input files without active user input, but using R function calls instead.
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bayesianbeastbeast2beautiphylogenetic-inferencephylogenetics
8.35 score 15 stars 5 dependents 223 scripts 645 downloadshillR - Diversity Through Hill Numbers
Calculate taxonomic, functional and phylogenetic diversity measures through Hill Numbers proposed by Chao, Chiu and Jost (2014) <doi:10.1146/annurev-ecolsys-120213-091540>.
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biodiversityhill-numbers
7.92 score 35 stars 2 dependents 227 scripts 956 downloadsFossilSim - Simulation and Plots for Fossil and Taxonomy Data
Simulating and plotting taxonomy and fossil data on phylogenetic trees under mechanistic models of speciation, preservation and sampling.
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7.84 score 12 stars 2 dependents 88 scripts 534 downloadsips - Interfaces to Phylogenetic Software in R
Functions that wrap popular phylogenetic software for sequence alignment, masking of sequence alignments, and estimation of phylogenies and ancestral character states.
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7.64 score 12 stars 2 dependents 200 scripts 845 downloadstracerer - Tracer from R
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'Tracer' (<https://github.com/beast-dev/tracer/>) is a GUI tool to parse and analyze the files generated by 'BEAST2'. This package provides a way to parse and analyze 'BEAST2' input files without active user input, but using R function calls instead.
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cpp
7.61 score 8 stars 3 dependents 80 scripts 481 downloadsRogue - Identify Rogue Taxa in Sets of Phylogenetic Trees
Rogue ("wildcard") taxa are leaves with uncertain phylogenetic position. Their position may vary from tree to tree under inference methods that yield a tree set (e.g. bootstrapping, Bayesian tree searches, maximum parsimony). The presence of rogue taxa in a tree set can potentially remove all information from a consensus tree. The information content of a consensus tree - a function of its resolution and branch support values - can often be increased by removing rogue tips. 'Rogue' provides an explicitly information-theoretic approach to rogue detection (Smith 2022) <doi:10.1093/sysbio/syab099>, an interface to 'RogueNaRok' (Aberer et al. 2013) <doi:10.1093/sysbio/sys078>, and heuristics for measuring leaf instability.
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consensus-treephylogenetic-treesphylogeneticscpp
7.49 score 5 stars 2 dependents 169 scripts 1.1k downloads
Rphylopars - Phylogenetic Comparative Tools for Missing Data and Within-Species Variation
Tools for performing phylogenetic comparative methods for datasets with with multiple observations per species (intraspecific variation or measurement error) and/or missing data (Goolsby et al. 2017). Performs ancestral state reconstruction and missing data imputation on the estimated evolutionary model, which can be specified as Brownian Motion, Ornstein-Uhlenbeck, Early-Burst, Pagel's lambda, kappa, or delta, or a star phylogeny.
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openblascpp
7.41 score 34 stars 1 dependents 127 scripts 561 downloadsevobiR - Evolutionary Biology in R
Comparative analysis of continuous traits influencing discrete states, and utility tools to facilitate comparative analyses. Implementations of ABBA/BABA type statistics to test for introgression in genomic data.
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comparative-methodsevolutionary-biologyphylogenetics
7.32 score 22 stars 113 scripts 117 downloads
entropart - Entropy Partitioning to Measure Diversity
Measurement and partitioning of diversity, based on Tsallis entropy, following Marcon and Herault (2015) <doi:10.18637/jss.v067.i08>. 'entropart' provides functions to calculate alpha, beta and gamma diversity of communities, including phylogenetic and functional diversity. Estimation-bias corrections are available.
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biodiversitydiversityentropy-partitioningestimatormeasurespecies
7.30 score 10 stars 1 dependents 133 scripts 575 downloadstreedater - Fast Molecular Clock Dating of Phylogenetic Trees with Rate Variation
Functions for estimating times of common ancestry and molecular clock rates of evolution using a variety of evolutionary models, parametric and nonparametric bootstrap confidence intervals, methods for detecting outlier lineages, root-to-tip regression, and a statistical test for selecting molecular clock models. For more details see Volz and Frost (2017) <doi:10.1093/ve/vex025>.
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7.13 score 29 stars 92 scripts 431 downloadsTreeSearch - Phylogenetic Analysis with Discrete Character Data
Reconstruct phylogenetic trees from discrete data. Inapplicable character states are handled using the algorithm of Brazeau, Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083> with the "Morphy" library, under equal or implied step weights. Contains a "shiny" user interface for interactive tree search and exploration of results, including character visualization, rogue taxon detection, tree space mapping, and cluster consensus trees (Smith 2022a, b) <doi:10.1093/sysbio/syab099>, <doi:10.1093/sysbio/syab100>. Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>, Successive Approximations (Farris, 1969) <doi:10.2307/2412182> and custom optimality criteria are implemented.
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bioinformaticsmorphological-analysisphylogeneticsresearch-tooltree-searchcpp
6.75 score 9 stars 121 scripts 1.1k downloadsbeastier - Call 'BEAST2'
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAST2' is a command-line tool. This package provides a way to call 'BEAST2' from an 'R' function call.
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bayesianbeastbeast2phylogenetic-inferencephylogeneticsopenjdk
6.60 score 11 stars 4 dependents 496 downloads
aphylo - Statistical Inference and Prediction of Annotations in Phylogenetic Trees
Implements a parsimonious evolutionary model to analyze and predict gene-functional annotations in phylogenetic trees as described in Vega Yon et al. (2021) <doi:10.1371/journal.pcbi.1007948>. Focusing on computational efficiency, 'aphylo' makes it possible to estimate pooled phylogenetic models, including thousands (hundreds) of annotations (trees) in the same run. The package also provides the tools for visualization of annotated phylogenies, calculation of posterior probabilities (prediction) and goodness-of-fit assessment featured in Vega Yon et al. (2021).
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annotationsinferencephylogeneticsrcpparmadillocpp
6.46 score 6 stars 96 scripts 592 downloadssecsse - Several Examined and Concealed States-Dependent Speciation and Extinction
Simultaneously infers state-dependent diversification across two or more states of a single or multiple traits while accounting for the role of a possible concealed trait. See Herrera-Alsina et al. (2019) <doi:10.1093/sysbio/syy057>.
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cpp
6.31 score 1 stars 34 scripts 454 downloads
ouch - Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses
Fit and compare Ornstein-Uhlenbeck models for evolution along a phylogenetic tree.
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adaptive-regimebrownian-motionornstein-uhlenbeckornstein-uhlenbeck-modelsouchphylogenetic-comparative-hypothesesphylogenetic-comparative-methodsphylogenetic-datareact
6.18 score 16 stars 4 dependents 75 scripts 1.1k downloadsratematrix - Bayesian Estimation of the Evolutionary Rate Matrix
The Evolutionary Rate Matrix is a variance-covariance matrix which describes both the rates of trait evolution and the evolutionary correlation among multiple traits. This package has functions to estimate these parameters using Bayesian MCMC. It is possible to test if the pattern of evolutionary correlations among traits has changed between predictive regimes painted along the branches of the phylogenetic tree. Regimes can be created a priori or estimated as part of the MCMC under a joint estimation approach. The package has functions to run MCMC chains, plot results, evaluate convergence, and summarize posterior distributions.
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openblascppopenmp
6.10 score 10 stars 1 dependents 28 scripts 409 downloads
phylotaR - Automated Phylogenetic Sequence Cluster Identification from 'GenBank'
A pipeline for the identification, within taxonomic groups, of orthologous sequence clusters from 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> as the first step in a phylogenetic analysis. The pipeline depends on a local alignment search tool and is, therefore, not dependent on differences in gene naming conventions and naming errors.
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blastngenbankpeer-reviewedphylogeneticssequence-alignment
6.03 score 25 stars 173 scripts 7 downloadsbayou - Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies
Fits and simulates multi-optima Ornstein-Uhlenbeck models to phylogenetic comparative data using Bayesian reversible-jump methods. See Uyeda and Harmon (2014) <DOI:10.1093/sysbio/syu057>.
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cpp
5.58 score 25 stars 76 scripts 449 downloadsAnnotationBustR - Extract Subsequences from GenBank Annotations
Extraction of subsequences into FASTA files from GenBank annotations where gene names may vary among accessions. Borstein & O'Meara (2018) <doi:10.7717/peerj.5179>.
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5.39 score 5 stars 11 scripts 1.3k downloadsTBRDist - Rearrangement Distances Between Phylogenetic Trees
Fast calculation of tree rearrangement distances. For unrooted trees: Subtree Prune and Regraft (SPR), Tree Bisection and Reconnection (TBR), and Replug distances, using the algorithms of Whidden and Matsen (2017) <doi:10.48550/arXiv.1511.07529>. For rooted trees: rooted SPR (rSPR) distance, using the fixed-parameter algorithms of Whidden, Beiko, and Zeh (2013) <doi:10.1137/110845045>.
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phylogeneticstree-distancealgorithmsbioinformaticsdistance-calculationphylogenetic-treescpp
4.78 score 1 stars 3 scripts 464 downloadsmcmc3r - Tools to work with MCMCtree and BPP
Tools to work with MCMCtree, a program for Bayesian inference of species divergence times.
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4.66 score 7 stars 11 scriptsdietr - Diet Estimated Trophic Levels
Estimates fractional trophic level from quantitative and qualitative diet data and calculates electivity indices in R. Borstein (2020) <doi:10.1007/s10750-020-04417-5>.
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dietelectivitytrophic
4.48 score 6 stars 375 downloadsRevticulate - Interaction with "RevBayes" in R
Interaction with "RevBayes" via R. Objects created in "RevBayes" can be passed into the R environment, and many types can be converted into similar R objects. To download "RevBayes", go to <https://revbayes.github.io/download>.
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3.72 score 9 stars 29 scripts 303 downloadsidendr0 - Interactive Dendrograms
Interactive dendrogram that enables the user to select and color clusters, to zoom and pan the dendrogram, and to visualize the clustered data not only in a built-in heat map, but also in 'GGobi' interactive plots and user-supplied plots. This is a backport of Qt-based 'idendro' (<https://github.com/tsieger/idendro>) to base R graphics and Tcl/Tk GUI.
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3.40 score 7 stars 36 scripts 455 downloadsPHYLOGR - Functions for Phylogenetically Based Statistical Analyses
Manipulation and analysis of phylogenetically simulated data sets and phylogenetically based analyses using GLS.
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3.02 score 26 scripts 344 downloadsdendextend - Extending 'dendrogram' Functionality in R
Offers a set of functions for extending 'dendrogram' objects in R, letting you visualize and compare trees of 'hierarchical clusterings'. You can (1) Adjust a tree's graphical parameters - the color, size, type, etc of its branches, nodes and labels. (2) Visually and statistically compare different 'dendrograms' to one another.
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16.21 score 161 stars 189 dependents 7.4k scripts 80k downloadsphylobase - Base Package for Phylogenetic Structures and Comparative Data
Provides a base S4 class for comparative methods, incorporating one or more trees and trait data.
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phylogeneticscpp
11.67 score 20 stars 18 dependents 836 scripts 8.7k downloads
RNeXML - Semantically Rich I/O for the 'NeXML' Format
Provides access to phyloinformatic data in 'NeXML' format. The package should add new functionality to R such as the possibility to manipulate 'NeXML' objects in more various and refined way and compatibility with 'ape' objects.
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metadatanexmlphylogeneticslinked-data
9.25 score 15 stars 19 dependents 7.6k downloadsdiversitree - Comparative 'Phylogenetic' Analyses of Diversification
Contains a number of comparative 'phylogenetic' methods, mostly focusing on analysing diversification and character evolution. Contains implementations of 'BiSSE' (Binary State 'Speciation' and Extinction) and its unresolved tree extensions, 'MuSSE' (Multiple State 'Speciation' and Extinction), 'QuaSSE', 'GeoSSE', and 'BiSSE-ness' Other included methods include Markov models of discrete and continuous trait evolution and constant rate 'speciation' and extinction.
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fftw3gslopenblascpp
9.24 score 33 stars 4 dependents 798 scripts 3.6k downloadsadephylo - Exploratory Analyses for the Phylogenetic Comparative Method
Multivariate tools to analyze comparative data, i.e. a phylogeny and some traits measured for each taxa. The package contains functions to represent comparative data, compute phylogenetic proximities, perform multivariate analysis with phylogenetic constraints and test for the presence of phylogenetic autocorrelation. The package is described in Jombart et al (2010) <doi:10.1093/bioinformatics/btq292>.
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8.65 score 10 stars 4 dependents 562 scripts 6.5k downloadsphylogram - Dendrograms for Evolutionary Analysis
Contains functions for developing phylogenetic trees as deeply-nested lists ("dendrogram" objects). Enables bi-directional conversion between dendrogram and "phylo" objects (see Paradis et al (2004) <doi:10.1093/bioinformatics/btg412>), and features several tools for command-line tree manipulation and import/export via Newick parenthetic text.
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peer-reviewed
7.67 score 12 stars 10 dependents 259 scripts 870 downloadstreespace - Statistical Exploration of Landscapes of Phylogenetic Trees
Tools for the exploration of distributions of phylogenetic trees. This package includes a 'shiny' interface which can be started from R using treespaceServer(). For further details see Jombart et al. (2017) <DOI:10.1111/1755-0998.12676>.
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cpp
7.53 score 30 stars 81 scripts 834 downloadsphylosignal - Exploring the Phylogenetic Signal in Continuous Traits
A collection of tools to explore the phylogenetic signal in univariate and multivariate data. The package provides functions to plot traits data against a phylogenetic tree, different measures and tests for the phylogenetic signal, methods to describe where the signal is located and a phylogenetic clustering method.
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openblascpp
7.42 score 19 stars 139 scripts 494 downloadsphylocomr - Interface to 'Phylocom'
Interface to 'Phylocom' (<https://phylodiversity.net/phylocom/>), a library for analysis of 'phylogenetic' community structure and character evolution. Includes low level methods for interacting with the three executables, as well as higher level interfaces for methods like 'aot', 'ecovolve', 'bladj', 'phylomatic', and more.
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phylogenyphylocomphylodiversitycommunity structurecharacter evolutionspeciescommunity-ecologyecologyevolution
6.78 score 15 stars 3 dependents 18 scripts 276 downloadstreebase - Discovery, Access and Manipulation of 'TreeBASE' Phylogenies
Interface to the API for 'TreeBASE' <http://treebase.org> from 'R.' 'TreeBASE' is a repository of user-submitted phylogenetic trees (of species, population, or genes) and the data used to create them.
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6.70 score 10 stars 1 dependents 56 scripts 602 downloads
phylotools - Phylogenetic Tools for Eco-Phylogenetics
A collection of tools for building RAxML supermatrix using PHYLIP or aligned FASTA files. These functions will be useful for building large phylogenies using multiple markers.
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6.60 score 15 stars 532 scripts 69 downloadssensiPhy - Sensitivity Analysis for Comparative Methods
An implementation of sensitivity analysis for phylogenetic comparative methods. The package is an umbrella of statistical and graphical methods that estimate and report different types of uncertainty in PCM: (i) Species Sampling uncertainty (sample size; influential species and clades). (ii) Phylogenetic uncertainty (different topologies and/or branch lengths). (iii) Data uncertainty (intraspecific variation and measurement error).
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comparative-methodsecologyevolutionphylogeneticssensitivity-analysis
6.45 score 14 stars 67 scripts 322 downloadsRevGadgets - Visualization and Post-Processing of 'RevBayes' Analyses
Processes and visualizes the output of complex phylogenetic analyses from the 'RevBayes' phylogenetic graphical modeling software.
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6.27 score 14 stars 295 scripts 307 downloadsbold - Interface to Bold Systems API
A programmatic interface to the Web Service methods provided by Bold Systems (<http://www.boldsystems.org/>) for genetic 'barcode' data. Functions include methods for searching by sequences by taxonomic names, ids, collectors, and institutions; as well as a function for searching for specimens, and downloading trace files.
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biodiversitybarcodednasequencesfastaapi-wrapperbarcodestaxize
6.02 score 21 stars 1 dependents 62 scripts 257 downloadsapex - Phylogenetic Methods for Multiple Gene Data
Toolkit for the analysis of multiple gene data (Jombart et al. 2017) <doi:10.1111/1755-0998.12567>. 'apex' implements the new S4 classes 'multidna', 'multiphyDat' and associated methods to handle aligned DNA sequences from multiple genes.
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5.89 score 5 stars 2.1k downloadsEvoPhylo - Pre- And Postprocessing of Morphological Data from Relaxed Clock Bayesian Phylogenetics
Performs automated morphological character partitioning for phylogenetic analyses and analyze macroevolutionary parameter outputs from clock (time-calibrated) Bayesian inference analyses, following concepts introduced by Simões and Pierce (2021) <doi:10.1038/s41559-021-01532-x>.
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5.89 score 4 stars 32 scripts 422 downloadsstrap - Stratigraphic Tree Analysis for Palaeontology
Functions for the stratigraphic analysis of phylogenetic trees.
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5.81 score 2 stars 3 dependents 71 scripts 703 downloadsFishPhyloMaker - Phylogenies for a List of Finned-Ray Fishes
Provides an alternative to facilitate the construction of a phylogeny for fish species from a list of species or a community matrix using as a backbone the phylogenetic tree proposed by Rabosky et al. (2018) <doi:10.1038/s41586-018-0273-1>.
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5.78 score 10 stars 20 scripts 357 downloadspaleoTS - Analyze Paleontological Time-Series
Facilitates analysis of paleontological sequences of trait values. Functions are provided to fit, using maximum likelihood, simple evolutionary models (including unbiased random walks, directional evolution,stasis, Ornstein-Uhlenbeck, covariate-tracking) and complex models (punctuation, mode shifts).
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5.56 score 1 stars 2 dependents 241 scripts 596 downloadsphylocanvas - Interactive Phylogenetic Trees Using the 'Phylocanvas' JavaScript Library
Create and customize interactive phylogenetic trees using the 'phylocanvas' JavaScript library and the 'htmlwidgets' package. These trees can be used directly from the R console, from 'RStudio', in Shiny apps, and in R Markdown documents. See <http://phylocanvas.org/> for more information on the 'phylocanvas' library.
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htmlwidgetsphylogeny
5.32 score 9 stars 23 scripts 263 downloads
MonoPhy - Explore Monophyly of Taxonomic Groups in a Phylogeny
Requires rooted phylogeny as input and creates a table of genera, their monophyly-status, which taxa cause problems in monophyly etc. Different information can be extracted from the output and a plot function allows visualization of the results in a number of ways. "MonoPhy: a simple R package to find and visualize monophyly issues." Schwery, O. & O'Meara, B.C. (2016) <doi:10.7717/peerj-cs.56>.
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5.08 score 8 stars 30 scripts 392 downloadstreeplyr - 'dplyr' Functionality for Matched Tree and Data Objects
Matches phylogenetic trees and trait data, and allows simultaneous manipulation of the tree and data using 'dplyr'.
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cpp
4.94 score 33 stars 131 scripts 33 downloadspmc - Phylogenetic Monte Carlo
Monte Carlo based model choice for applied phylogenetics of continuous traits. Method described in Carl Boettiger, Graham Coop, Peter Ralph (2012) Is your phylogeny informative? Measuring the power of comparative methods, Evolution 66 (7) 2240-51. <doi:10.1111/j.1558-5646.2011.01574.x>.
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4.68 score 2 stars 12 scripts 472 downloadspaleobuddy - Simulating Diversification Dynamics
Simulation of species diversification, fossil records, and phylogenies. While the literature on species birth-death simulators is extensive, including important software like 'paleotree' and 'APE', we concluded there were interesting gaps to be filled regarding possible diversification scenarios. Here we strove for flexibility over focus, implementing a large array of regimens for users to experiment with and combine. In this way, 'paleobuddy' can be used in complement to other simulators as a flexible jack of all trades, or, in the case of scenarios implemented only here, can allow for robust and easy simulations for novel situations. Environmental data modified from that in 'RPANDA': Morlon H. et al (2016) <doi:10.1111/2041-210X.12526>.
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evolutionmacroevolutionpaleobiologypaleontologyphylogenetics
4.65 score 9 stars 9 scripts 244 downloadsDAMOCLES - Dynamic Assembly Model of Colonization, Local Extinction and Speciation
Simulates and computes (maximum) likelihood of a dynamical model of community assembly that takes into account phylogenetic history.
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cpp
4.30 score 2 stars 10 scripts 323 downloadsbrranching - Fetch 'Phylogenies' from Many Sources
Includes methods for fetching 'phylogenies' from a variety of sources, including the 'Phylomatic' web service (<http://phylodiversity.net/phylomatic/>), and 'Phylocom' (<https://github.com/phylocom/phylocom/>).
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phylogenytreephylomaticmolecularplantsphylogenies
4.23 score 20 stars 34 scripts 82 downloadsepm - EcoPhyloMapper
Facilitates the aggregation of species' geographic ranges from vector or raster spatial data, and that enables the calculation of various morphological and phylogenetic community metrics across geography. Citation: Title, PO, DL Swiderski and ML Zelditch (2022) <doi:10.1111/2041-210X.13914>.
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cpp
4.23 score 16 stars 21 scripts 454 downloadsphyloTop - Calculating Topological Properties of Phylogenies
Tools for calculating and viewing topological properties of phylogenetic trees.
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3.79 score 1 stars 62 scripts 477 downloads
nodeSub - Simulate DNA Alignments Using Node Substitutions
Simulate DNA sequences for the node substitution model. In the node substitution model, substitutions accumulate additionally during a speciation event, providing a potential mechanistic explanation for substitution rate variation. This package provides tools to simulate such a process, simulate a reference process with only substitutions along the branches, and provides tools to infer phylogenies from alignments. More information can be found in Janzen (2021) <doi:10.1093/sysbio/syab085>.
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cppopenjdk
2.70 score 1 stars 5 scripts 466 downloadsbppr - An R package for BPP
Functions to work with the multi-species coalescent program BPP, for example, functions to calibrate BPP trees to geological time.
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2.60 score 8 stars 1 scriptsselac - Selection Models for Amino Acid and/or Codon Evolution
Sets up and executes a SelAC model (Selection on Amino acids and codons) for testing the presence of selection in amino acid or codon among a set of genes on a fixed phylogeny. Beaulieu et al (2019) <doi:10.1093/molbev/msy222>.
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2.40 score 1 stars 11 downloadslaser - Likelihood Analysis of Speciation/Extinction Rates from Phylogenies
laser implements maximum likelihood methods based on the birth-death process to test whether diversification rates have changed over time and whether rates vary among lineages.
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2.08 score 2 stars 60 scripts 23 downloads