vegan - Community Ecology Package

Ordination methods, diversity analysis and other functions for community and vegetation ecologists.

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ecological-modellingecologyordinationopenblasfortran

19.86 score 533 stars 504 dependents 25k scripts 147k 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

17.10 score 1.4k stars 41 dependents 23k scripts 41k 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

17.03 score 214 stars 134 dependents 4.0k scripts 26k downloads

ape - Analyses of Phylogenetics and Evolution

Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle, MAFFT) whose results are returned into R.

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openblascpp

16.04 score 74 stars 660 dependents 23k scripts 134k downloads

phytools - Phylogenetic Tools for Comparative Biology (and Other Things)

A wide range of methods for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous techniques for visualizing, analyzing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and trait data. A broad range of plotting methods for phylogenies and comparative data include (but are not restricted to) methods for mapping trait evolution on trees, for projecting trees into phenotype space or a onto a geographic map, and for visualizing correlated speciation between trees. Lastly, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for computing consensus phylogenies from a set, for simulating phylogenetic trees and data under a range of models, for randomly or non-randomly attaching species or clades to a tree, as well as for a wide range of other manipulations and analyses that phylogenetic biologists might find useful in their research.

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13.74 score 232 stars 84 dependents 7.2k scripts 16k downloads

taxize - 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

13.03 score 298 stars 11 dependents 1.7k scripts 9.4k downloads

tidytree - A Tidy Tool for Phylogenetic Tree Data Manipulation

Phylogenetic tree generally contains multiple components including node, edge, branch and associated data. 'tidytree' provides an approach to convert tree object to tidy data frame as well as provides tidy interfaces to manipulate tree data.

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phylogenetic-treetidyversetree-data

12.85 score 60 stars 135 dependents 864 scripts 56k 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

12.05 score 46 stars 14 dependents 450 scripts 8.6k downloads

TreeDist - 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, including the transfer consensus (Takazawa et al. 2026) <doi:10.64898/2026.03.16.712085>, and for computing the information content of trees and splits.

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phylogeneticstree-distancebioinformaticscladisticsentropyinformation-theorymutual-informationphylogenetic-treestree-distancestreescppopenmp

11.43 score 37 stars 11 dependents 166 scripts 2.7k downloads

phylolm - 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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11.22 score 36 stars 16 dependents 430 scripts 15k downloads

TreeTools - 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

11.17 score 24 stars 23 dependents 214 scripts 4.1k downloads

MCMCglmm - 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

11.04 score 5 stars 12 dependents 1.6k scripts 11k downloads

geomorph - 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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10.75 score 88 stars 4 dependents 932 scripts 3.2k 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

10.56 score 106 stars 3 dependents 404 scripts 793 downloads

mvMORPH - 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. See Clavel et al. (2015) <DOI:10.1111/2041-210X.12420>, Clavel et al. (2019) <DOI:10.1093/sysbio/syy045>, and Clavel & Morlon (2020) <DOI:10.1093/sysbio/syaa010>.

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openblas

9.98 score 19 stars 3 dependents 269 scripts 570 downloads

corHMM - 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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9.60 score 15 stars 2 dependents 563 scripts 653 downloads

OUwie - Analysis of Evolutionary Rates in an OU Framework

Estimates rates for continuous character evolution under Brownian motion and a new set of 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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9.13 score 10 stars 227 scripts 354 downloads

RRphylo - 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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8.72 score 11 stars 2 dependents 111 scripts 714 downloads

beautier - '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

8.61 score 13 stars 5 dependents 200 scripts 395 downloads

rncl - 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

8.43 score 9 stars 33 dependents 24 scripts 13k downloads

RRPP - Linear Model Evaluation with Randomized Residuals in a Permutation Procedure

Linear model calculations are made for many random versions of data. Using residual randomization in a permutation procedure, sums of squares are calculated over many permutations to generate empirical probability distributions for evaluating model effects. Additionally, coefficients, statistics, fitted values, and residuals generated over many permutations can be used for various procedures including pairwise tests, prediction, classification, and model comparison. This package should provide most tools one could need for the analysis of high-dimensional data, especially in ecology and evolutionary biology, but certainly other fields, as well.

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8.33 score 4 stars 5 dependents 205 scripts 1.5k downloads

dispRity - 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

8.21 score 29 stars 1 dependents 256 scripts 889 downloads

evobiR - 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

8.14 score 21 stars 124 scripts 32 downloads

hillR - 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

8.08 score 36 stars 3 dependents 214 scripts 780 downloads

hisse - 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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8.02 score 7 stars 208 scripts 357 downloads

FossilSim - 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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7.92 score 12 stars 2 dependents 80 scripts 378 downloads

Quartet - 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>; these distances can be used to construct consensus trees via the greedy heuristic of Takazawa et al. (2026), Outperforming the majority-rule consensus tree using fine-grained dissimilarity measures, bioRxiv <doi:10.64898/2026.03.16.712085>.

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bioinformaticscomparisonphylogenetic-treesphylogeneticsquartetquartet-distanceresearch-tooltreecppopenmp

7.85 score 17 stars 55 scripts 1.1k downloads

beastier - 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

7.61 score 11 stars 4 dependents 52 scripts 379 downloads

tracerer - 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

7.54 score 8 stars 3 dependents 80 scripts 319 downloads

treespace - 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

7.51 score 29 stars 79 scripts 256 downloads

treedater - 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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7.46 score 27 stars 71 scripts 215 downloads

Claddis - Measuring Morphological Diversity and Evolutionary Tempo

Measures morphological diversity from discrete character data and estimates evolutionary tempo on phylogenetic trees. Imports morphological data from #NEXUS (Maddison et al. (1997) <doi:10.1093/sysbio/46.4.590>) format with read_nexus_matrix(), and writes to both #NEXUS and TNT format (Goloboff et al. (2008) <doi:10.1111/j.1096-0031.2008.00217.x>). Main functions are test_rates(), which implements AIC and likelihood ratio tests for discrete character rates introduced across Lloyd et al. (2012) <doi:10.1111/j.1558-5646.2011.01460.x>, Brusatte et al. (2014) <doi:10.1016/j.cub.2014.08.034>, Close et al. (2015) <doi:10.1016/j.cub.2015.06.047>, and Lloyd (2016) <doi:10.1111/bij.12746>, and calculate_morphological_distances(), which implements multiple discrete character distance metrics from Gower (1971) <doi:10.2307/2528823>, Wills (1998) <doi:10.1006/bijl.1998.0255>, Lloyd (2016) <doi:10.1111/bij.12746>, and Hopkins and St John (2018) <doi:10.1098/rspb.2018.1784>. This also includes the GED correction from Lehmann et al. (2019) <doi:10.1111/pala.12430>. Multiple functions implement morphospace plots: plot_chronophylomorphospace() implements Sakamoto and Ruta (2012) <doi:10.1371/journal.pone.0039752>, plot_morphospace() implements Wills et al. (1994) <doi:10.1017/S009483730001263X>, plot_changes_on_tree() implements Wang and Lloyd (2016) <doi:10.1098/rspb.2016.0214>, and plot_morphospace_stack() implements Foote (1993) <doi:10.1017/S0094837300015864>. Other functions include safe_taxonomic_reduction(), which implements Wilkinson (1995) <doi:10.1093/sysbio/44.4.501>, map_dollo_changes() implements the Dollo stochastic character mapping of Tarver et al. (2018) <doi:10.1093/gbe/evy096>, and estimate_ancestral_states() implements the ancestral state options of Lloyd (2018) <doi:10.1111/pala.12380>. calculate_tree_length() and reconstruct_ancestral_states() implements the generalised algorithms from Swofford and Maddison (1992; no doi).

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7.38 score 14 stars 2 dependents 80 scripts 446 downloads

Rogue - 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 taxa. 'Rogue' provides an explicitly information-theoretic approach to rogue detection (Smith 2022) <doi:10.1093/sysbio/syab099>, and an interface to 'RogueNaRok' (Aberer et al. 2013) <doi:10.1093/sysbio/sys078>.

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consensus-treephylogenetic-treesphylogenetics

7.26 score 4 stars 2 dependents 149 scripts 1.1k 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

7.21 score 9 stars 1 dependents 119 scripts 532 downloads

aphid - Analysis with Profile Hidden Markov Models

Designed for the development and application of hidden Markov models and profile HMMs for biological sequence analysis. Contains functions for multiple and pairwise sequence alignment, model construction and parameter optimization, file import/export, implementation of the forward, backward and Viterbi algorithms for conditional sequence probabilities, tree-based sequence weighting, and sequence simulation. Features a wide variety of potential applications including database searching, gene-finding and annotation, phylogenetic analysis and sequence classification. Based on the models and algorithms described in Durbin et al (1998, ISBN: 9780521629713).

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cpp

7.09 score 22 stars 4 dependents 47 scripts 592 downloads

ips - 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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6.66 score 12 stars 2 dependents 159 scripts 665 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

6.49 score 6 stars 104 scripts 610 downloads

TreeSearch - 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

6.49 score 9 stars 44 scripts 879 downloads

secsse - 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

6.43 score 1 stars 34 scripts 289 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

6.43 score 16 stars 4 dependents 70 scripts 413 downloads

treedata.table - Manipulation of Matched Phylogenies and Data using 'data.table'

An implementation that combines trait data and a phylogenetic tree (or trees) into a single object of class 'treedata.table'. The resulting object can be easily manipulated to simultaneously change the trait- and tree-level sampling. Currently implemented functions allow users to use a 'data.table' syntax when performing operations on the trait dataset within the 'treedata.table' object. For more details see Roman-Palacios et al. (2021) <doi:10.7717/peerj.12450>.

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6.40 score 7 stars 24 scripts 180 downloads

datelife - Scientific Data on Time of Lineage Divergence for Your Taxa

Methods and workflows to get chronograms (i.e., phylogenetic trees with branch lengths proportional to time), using open, peer-reviewed, state-of-the-art scientific data on time of lineage divergence. This package constitutes the main underlying code of the DateLife web service at <https://www.datelife.org>. To obtain a single summary chronogram from a group of relevant chronograms, we implement the Super Distance Matrix (SDM) method described in Criscuolo et al. (2006) <doi:10.1080/10635150600969872>. To find the grove of chronograms with a sufficiently overlapping set of taxa for summarizing, we implement theorem 1.1. from Ané et al. (2009) <doi:10.1007/s00026-009-0017-x>. A given phylogenetic tree can be dated using time of lineage divergence data as secondary calibrations (with caution, see Schenk (2016) <doi:10.1371/journal.pone.0148228>). To obtain and apply secondary calibrations, the package implements the congruification method described in Eastman et al. (2013) <doi:10.1111/2041-210X.12051>. Tree dating can be performed with different methods including BLADJ (Webb et al. (2008) <doi:10.1093/bioinformatics/btn358>), PATHd8 (Britton et al. (2007) <doi:10.1080/10635150701613783>), mrBayes (Huelsenbeck and Ronquist (2001) <doi:10.1093/bioinformatics/17.8.754>), and treePL (Smith and O'Meara (2012) <doi:10.1093/bioinformatics/bts492>).

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softwaredating-softwareevolutionphylogeneticsreproducible-research

6.17 score 14 stars 66 scripts 60 downloads

ratematrix - 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 256 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

6.01 score 25 stars 163 scripts 1 downloads

EvoPhylo - 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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5.81 score 4 stars 27 scripts 212 downloads

bayou - 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

5.65 score 24 stars 92 scripts 230 downloads

mcmc3r - 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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4.72 score 7 stars 9 scripts

TBRDist - 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

4.60 score 1 stars 4 scripts 614 downloads

AnnotationBustR - 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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4.48 score 5 stars 12 scripts 316 downloads

epm - 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

4.46 score 16 stars 18 scripts 303 downloads

DAMOCLES - 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

4.04 score 1 stars 11 scripts 255 downloads

phyloTop - 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 398 downloads

Revticulate - 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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3.69 score 9 stars 27 scripts 267 downloads

idendr0 - 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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3.21 score 7 stars 23 scripts 645 downloads

PHYLOGR - 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 209 downloads

dendextend - 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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16.81 score 160 stars 181 dependents 8.9k scripts 93k downloads

picante - 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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11.83 score 39 stars 13 dependents 1.4k scripts 9.1k downloads

phylobase - 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

11.57 score 20 stars 19 dependents 638 scripts 8.6k 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

10.32 score 15 stars 20 dependents 101 scripts 8.3k downloads

geiger - Analysis of Evolutionary Diversification

Methods for fitting macroevolutionary models to phylogenetic trees Pennell (2014) <doi:10.1093/bioinformatics/btu181>.

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openblascpp

10.17 score 26 stars 29 dependents 2.6k scripts 6.3k downloads

phyclust - Phylogenetic Clustering (Phyloclustering)

Phylogenetic clustering (phyloclustering) is an evolutionary Continuous Time Markov Chain model-based approach to identify population structure from molecular data without assuming linkage equilibrium. The package phyclust (Chen 2011) provides a convenient implementation of phyloclustering for DNA and SNP data, capable of clustering individuals into subpopulations and identifying molecular sequences representative of those subpopulations. It is designed in C for performance, interfaced with R for visualization, and incorporates other popular open source programs including ms (Hudson 2002) <doi:10.1093/bioinformatics/18.2.337>, seq-gen (Rambaut and Grassly 1997) <doi:10.1093/bioinformatics/13.3.235>, Hap-Clustering (Tzeng 2005) <doi:10.1002/gepi.20063> and PAML baseml (Yang 1997, 2007) <doi:10.1093/bioinformatics/13.5.555>, <doi:10.1093/molbev/msm088>, for simulating data, additional analyses, and searching the best tree. See the phyclust website for more information, documentations and examples.

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8.71 score 10 stars 8 dependents 199 scripts 2.2k downloads

adephylo - 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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8.56 score 10 stars 4 dependents 520 scripts 5.8k downloads

diversitree - 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

8.55 score 33 stars 4 dependents 600 scripts 585 downloads

paleotree - Paleontological and Phylogenetic Analyses of Evolution

Provides tools for transforming, a posteriori time-scaling, and modifying phylogenies containing extinct (i.e. fossil) lineages. In particular, most users are interested in the functions timePaleoPhy, bin_timePaleoPhy, cal3TimePaleoPhy and bin_cal3TimePaleoPhy, which date cladograms of fossil taxa using stratigraphic data. This package also contains a large number of likelihood functions for estimating sampling and diversification rates from different types of data available from the fossil record (e.g. range data, occurrence data, etc). paleotree users can also simulate diversification and sampling in the fossil record using the function simFossilRecord, which is a detailed simulator for branching birth-death-sampling processes composed of discrete taxonomic units arranged in ancestor-descendant relationships. Users can use simFossilRecord to simulate diversification in incompletely sampled fossil records, under various models of morphological differentiation (i.e. the various patterns by which morphotaxa originate from one another), and with time-dependent, longevity-dependent and/or diversity-dependent rates of diversification, extinction and sampling. Additional functions allow users to translate simulated ancestor-descendant data from simFossilRecord into standard time-scaled phylogenies or unscaled cladograms that reflect the relationships among taxon units.

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7.77 score 22 stars 3 dependents 298 scripts 948 downloads

phylogram - 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

7.74 score 12 stars 10 dependents 259 scripts 1.2k downloads

phylosignal - 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

7.66 score 19 stars 120 scripts 450 downloads

phyloregion - Biogeographic Regionalization and Macroecology

Computational infrastructure for biogeography, community ecology, and biodiversity conservation (Daru et al. 2020) <doi:10.1111/2041-210X.13478>. It is based on the methods described in Daru et al. (2020) <doi:10.1038/s41467-020-15921-6>. The original conceptual work is described in Daru et al. (2017) <doi:10.1016/j.tree.2017.08.013> on patterns and processes of biogeographical regionalization. Additionally, the package contains fast and efficient functions to compute more standard conservation measures such as phylogenetic diversity, phylogenetic endemism, evolutionary distinctiveness and global endangerment, as well as compositional turnover (e.g., beta diversity).

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software

7.52 score 20 stars 1 dependents 73 scripts 475 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

7.07 score 32 stars 1 dependents 121 scripts 521 downloads

apex - 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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7.06 score 5 stars 60 scripts 5.1k downloads

phylocomr - 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

6.88 score 15 stars 4 dependents 17 scripts 204 downloads

treebase - 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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6.65 score 10 stars 1 dependents 50 scripts 288 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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6.58 score 15 stars 509 scripts 25 downloads

sensiPhy - 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 15 stars 62 scripts 214 downloads

RevGadgets - 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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6.24 score 14 stars 276 scripts 291 downloads

bold - 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

6.09 score 21 stars 1 dependents 73 scripts 206 downloads

strap - Stratigraphic Tree Analysis for Palaeontology

Functions for the stratigraphic analysis of phylogenetic trees.

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5.82 score 2 stars 3 dependents 74 scripts 994 downloads

FishPhyloMaker - 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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5.71 score 10 stars 17 scripts 262 downloads

paleoTS - 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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5.49 score 1 stars 2 dependents 206 scripts 393 downloads

phylocanvas - 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

5.43 score 9 stars 30 scripts 216 downloads

TreeSim - Simulating Phylogenetic Trees

Simulation methods for phylogenetic trees where (i) all tips are sampled at one time point or (ii) tips are sampled sequentially through time. (i) For sampling at one time point, simulations are performed under a constant rate birth-death process, conditioned on having a fixed number of final tips (sim.bd.taxa()), or a fixed age (sim.bd.age()), or a fixed age and number of tips (sim.bd.taxa.age()). When conditioning on the number of final tips, the method allows for shifts in rates and mass extinction events during the birth-death process (sim.rateshift.taxa()). The function sim.bd.age() (and sim.rateshift.taxa() without extinction) allow the speciation rate to change in a density-dependent way. The LTT plots of the simulations can be displayed using LTT.plot(), LTT.plot.gen() and LTT.average.root(). TreeSim further samples trees with n final tips from a set of trees generated by the common sampling algorithm stopping when a fixed number m>>n of tips is first reached (sim.gsa.taxa()). This latter method is appropriate for m-tip trees generated under a big class of models (details in the sim.gsa.taxa() man page). For incomplete phylogeny, the missing speciation events can be added through simulations (corsim()). (ii) sim.rateshifts.taxa() is generalized to sim.bdsky.stt() for serially sampled trees, where the trees are conditioned on either the number of sampled tips or the age. Furthermore, for a multitype-branching process with sequential sampling, trees on a fixed number of tips can be simulated using sim.bdtypes.stt.taxa(). This function further allows to simulate under epidemiological models with an exposed class. The function sim.genespeciestree() simulates coalescent gene trees within birth-death species trees, and sim.genetree() simulates coalescent gene trees.

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fortran

5.09 score 1 stars 3 dependents 344 scripts 4.0k 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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4.99 score 7 stars 28 scripts 138 downloads

treeplyr - '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

4.91 score 33 stars 124 scripts 29 downloads

dietr - 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

4.84 score 6 stars 23 scripts 302 downloads

brranching - 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

4.74 score 20 stars 1 dependents 37 scripts 70 downloads

paleobuddy - 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 3 scripts 210 downloads

pmc - 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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4.64 score 2 stars 11 scripts 274 downloads

TreEvo - Using ABC to Understand Trait Evolution

Various functions for estimating parameters of trait evolution in comparative analyses using Approximate Bayesian Computation.

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4.11 score 1 stars 65 scripts

phyloclim - Integrating Phylogenetics and Climatic Niche Modeling

Implements some methods in phyloclimatic modeling: estimation of ancestral climatic niches, age-range-correlation, niche equivalency test and background-similarity test.

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4.01 score 5 stars 41 scripts 16 downloads

apTreeshape - Analyses of Phylogenetic Treeshape

Simulation and analysis of phylogenetic tree topologies using statistical indices. It is a companion library of the 'ape' package. It provides additional functions for reading, plotting, manipulating phylogenetic trees. It also offers convenient web-access to public databases, and enables testing null models of macroevolution using corrected test statistics. Trees of class "phylo" (from 'ape' package) can be converted easily. Implements methods described in Bortolussi et al. (2005) <doi:10.1093/bioinformatics/bti798> and Maliet et al. (2017) <doi:10.1101/224295>.

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3.89 score 154 scripts 120 downloads

nichevol - Tools for Ecological Niche Evolution Assessment Considering Uncertainty

A collection of tools that allow users to perform critical steps in the process of assessing ecological niche evolution over phylogenies, with uncertainty incorporated explicitly in reconstructions. The method proposed here for ancestral reconstruction of ecological niches characterizes species' niches using a bin-based approach that incorporates uncertainty in estimations. Compared to other existing methods, the approaches presented here reduce risk of overestimation of amounts and rates of ecological niche evolution. The main analyses include: initial exploration of environmental data in occurrence records and accessible areas, preparation of data for phylogenetic analyses, executing comparative phylogenetic analyses of ecological niches, and plotting for interpretations. Details on the theoretical background and methods used can be found in: Owens et al. (2020) <doi:10.1002/ece3.6359>, Peterson et al. (1999) <doi:10.1126/science.285.5431.1265>, Soberón and Peterson (2005) <doi:10.17161/bi.v2i0.4>, Peterson (2011) <doi:10.1111/j.1365-2699.2010.02456.x>, Barve et al. (2011) <doi:10.1111/ecog.02671>, Machado-Stredel et al. (2021) <doi:10.21425/F5FBG48814>, Owens et al. (2013) <doi:10.1016/j.ecolmodel.2013.04.011>, Saupe et al. (2018) <doi:10.1093/sysbio/syx084>, and Cobos et al. (2021) <doi:10.1111/jav.02868>.

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3.88 score 15 stars 5 scripts 140 downloads

phrapl - Phylogeography using Approximate Likelihood

This creates and compares models for population structure within a species or between several related species, especially for questions in phylogeography. It can also help delimit populations into species. Models used can range from island models (populations exchanging genes through migration) to phylogeny models (populations splitting with no subsequent gene flow) to anything in between, such as subdivision with some gene flow. Input data are gene tree topologies. Models are fit using approximate likelihood: simulating gene tree evolution many times on the various population trees to estimate the likelihood of seeing the observed gene topologies.

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3.78 score 8 stars 15 scripts

treeducken - Nested Phylogenetic Tree Simulator

Simulates nested phylogenetic trees (gene trees in species tree, symbiont trees in host trees) using birth-death processes and transfers between lineages. Simulations of gene trees within species trees are performed using a three-tree model with species trees, locus trees, and gene trees. The cophylogenetic birth-death process is used to simulate sets of host and symbiont trees with extant associations between tips. For more information about the three-tree model see: Mallo et al. (2015) <doi:10.1093/sysbio/syv082>, Rasmussen and Kellis (2012) <doi:10.1101/gr.123901.111>.

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cpp

3.72 score 4 stars 26 scripts 13 downloads

hilldiv - Integral Analysis of Diversity Based on Hill Numbers

Tools for analysing, comparing, visualising and partitioning diversity based on Hill numbers. 'hilldiv' is an R package that provides a set of functions to assist analysis of diversity for diet reconstruction, microbial community profiling or more general ecosystem characterisation analyses based on Hill numbers, using OTU/ASV tables and associated phylogenetic trees as inputs. The package includes functions for (phylo)diversity measurement, (phylo)diversity profile plotting, (phylo)diversity comparison between samples and groups, (phylo)diversity partitioning and (dis)similarity measurement. All of these grounded in abundance-based and incidence-based Hill numbers. The statistical framework developed around Hill numbers encompasses many of the most broadly employed diversity (e.g. richness, Shannon index, Simpson index), phylogenetic diversity (e.g. Faith's PD, Allen's H, Rao's quadratic entropy) and dissimilarity (e.g. Sorensen index, Unifrac distances) metrics. This enables the most common analyses of diversity to be performed while grounded in a single statistical framework. The methods are described in Jost et al. (2007) <DOI:10.1890/06-1736.1>, Chao et al. (2010) <DOI:10.1098/rstb.2010.0272> and Chiu et al. (2014) <DOI:10.1890/12-0960.1>; and reviewed in the framework of molecularly characterised biological systems in Alberdi & Gilbert (2019) <DOI:10.1111/1755-0998.13014>.

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3.62 score 12 stars 70 scripts 22 downloads

CALANGO - Comparative Analysis with Annotation-Based Genomic Components

A first-principle, phylogeny-aware comparative genomics tool for investigating associations between terms used to annotate genomic components (e.g., Pfam IDs, Gene Ontology terms,) with quantitative or rank variables such as number of cell types, genome size, or density of specific genomic elements. See the project website for more information, documentation and examples, and <doi:10.1016/j.patter.2023.100728> for the full paper.

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3.00 score 4 scripts 264 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 3 scripts 553 downloads

bppr - 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 scripts

windex - Analysing Convergent Evolution using the Wheatsheaf Index

Analysing convergent evolution using the Wheatsheaf index, described in Arbuckle et al. (2014) <doi: 10.1111/2041-210X.12195>, and some other unrelated but perhaps useful functions.

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2.60 score 9 scripts 207 downloads

dentist - Dents the Likelihood Surface to Estimate Parameter Uncertainty

This will sample points around a specified distance from the maximum likelihood estimates. This should be a better way to estimate uncertainty than using the Hessian of the likelihood equation. It works by "denting" the likelihood surface to make a ridge at the desired difference in log likelihood and then "walks" around this dented surface, sampling points.

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2.50 score 3 stars 21 scripts

selac - 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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2.65 score 1 stars 18 scripts 4 downloads

BMhyb - Comparative Methods for Phylogenetic Networks

Analyze the phenotypic evolution of species of hybrid origin on a phylogenetic network. This can detect a burst of variation at the formation of a hybrid as well as an increase or decrease in trait value at a hybridization event. Parameters are estimated by maximum likelihood, and model averaging can be done automatically. Users need to enter a comparative data set and a phylogenetic network.

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2.49 score 62 scripts 4 downloads

extendedSurface - Fit Complex Multi-OU Models by Extending SURFACE and Providing an Interface with OUwie

Multi Ornstein Uhlenbeck (OUM) models are routinely employed to describe the phenotypic evolution of clades across a macroevolutionary adaptive landscape. Multiple implementations exist, including those that require an a priori assigment of lineages to adaptive regimes (e.g., OUwie), and those that infer the location of such regimes shifts (e.g., SURFACE). However, SURFACE has been found to favor overly complex models, which is likely a consequence of fixing a single rate of evolution and force of attraction for the entire tree. Although these parameters can be optimized for each regime by using the SURFACE output as the set of regime shifts required by OUwie, such complex models often fail to be optimized. extendedSurface provides a solution by continuing the backwards phase of SURFACE, merging regimes and generating simpler (yet suboptimal) multiOU models. These are then fed to OUwie, where parameters for each regime can be independetly optimized. Using simpler OUM models as starting points improves the probability of successful model fitting. The resulting models are more realistic, and have been found to be favored over others using empirical comparative datasets. The package allows the user to decide which models should be fit (OUMA, OUMV, OUMVA, with and without stationary root state), and plots the fit of these against those explored by SURFACE to easily compare model fit. Additionally, several approaches to record and plot the evolutionary dynamics of discrete traits through time are also implemented.

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2.40 score 5 stars

rphylotastic - An R Interface to 'Phylotastic' Web Services

This wraps the 'Phylotastic' services APIs described on Web Services at <www.phylotastic.org>. The main use case is to return a phylogenetic tree for a set of species, but the services also include ways to extract species names from web pages, perform taxonomic name resolution, retrieve a list of all descendant species of a taxon, find images of a species, and more.

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2.28 score 19 scripts

laser - 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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2.06 score 2 stars 57 scripts 8 downloads

sisters - Runs various sister group comparisons to test hypotheses about diversification

Sister groups are pairs of clades that differ in a key character. If that character leads to higher diversification rate, then clades with that trait should have more species than their sisters. There are several tests to see if this is the case, ranging from a basic sign test to more complex ones (many implemented in the ape package). This package can identify sister groups that differ in a binary trait and perform all the relevant tests. It can also discretize a continuous trait into a binary "high" vs "low" state.

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2.00 score 2 stars 2 scripts

phybase - Basic functions for phylogenetic analysis

This package provides functions to read, write, manipulate, estimate, and summarize phylogenetic trees including species trees which contain not only the topology and branch lengths but also population sizes. The input/output functions can read tree files in which trees are presented in parenthetic format. The trees are read in as a string and then transformed to a matrix which describes the relationship of nodes and branch lengths. The nodes matrix provides an easy access for developers to further manipulate the tree, while the tree string provides interface with other phylogenetic R packages such as "ape". The input/output functions can also be used to change the format of tree files between NEXUS and PHYLIP. Some basic functions have already been established in the package for manipulating trees such as deleting and swapping nodes, rooting and unrooting trees, changing the root of the tree. The package also includes functions such as "consensus", "coaltime, "popsize", "treedist" for summarizing phylogenetic trees, calculating the coalescence time, population size, and tree distance. The function maxtree is built in the package to esimtate the species tree from multiple gene trees.

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1.92 score 83 scripts 2 downloads

TreePar - Estimating Birth and Death Rates Based on Phylogenies

(i) For a given species phylogeny on present day data which is calibrated to calendar-time, a method for estimating maximum likelihood speciation and extinction processes is provided. The method allows for non-constant rates. Rates may change (1) as a function of time, i.e. rate shifts at specified times or mass extinction events (likelihood implemented as LikShifts(), optimization as bd.shifts.optim() and visualized as bd.shifts.plot()) or (2) as a function of the number of species, i.e. density-dependence (likelihood implemented as LikDD() and optimization as bd.densdep.optim()) or (3) extinction rate may be a function of species age (likelihood implemented as LikAge() and optimization as bd.age.optim.matlab()). Note that the methods take into account the whole phylogeny, in particular it accounts for the "pull of the present" effect. (1-3) can take into account incomplete species sampling, as long as each species has the same probability of being sampled. For a given phylogeny on higher taxa (i.e. all but one species per taxa are missing), where the number of species is known within each higher taxa, speciation and extinction rates can be estimated under model (1) (implemented within LikShifts() and bd.shifts.optim() with groups !=0). (ii) For a given phylogeny with sequentially sampled tips, e.g. a virus phylogeny, rates can be estimated under a model where rates vary across time using bdsky.stt.optim() based on likelihood LikShiftsSTT() (extending LikShifts() and bd.shifts.optim()). Furthermore, rates may vary as a function of host types using LikTypesSTT() (multitype branching process extending functions in R package diversitree). This function can furthermore calculate the likelihood under an epidemiological model where infected individuals are first exposed and then infectious.

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1.71 score 51 scripts 16 downloads

closesamples - Gets feasible taxon samples on a tree

Often you want to pick species at random, but don't have access to all the possible species, and your group might be a nonrandom set. However, you might have a taxonomy, perhaps a bad one, for all the species. This will let you pick species at random on that full taxonomy and then pick a species out of the possible set closest to this. You could still have a biased sample, but way less biased.

Last updated

1.70 score

flipped - Applies various odd models for coin flipping

Everyone uses the binomial as the distribution for coin flipping: this assumes for a given coin, the probability of landing heads is constant for all time. It is likely a very sound assumption. However, even for this simple example other models may be possible. This package contains such models.

Last updated

1.70 score 4 scripts

popularitree - Subsamples a tree to get popular taxa

Often you want to show a reduced summary tree. Taxa chosen should span all the tree (for example, a tree of mammals should not have just primates) but also be recognizable groups to your audience. This lets you select a final tree size you want, criteria you want to use, and finds the tree that maximizes the criteria.

Last updated

1.70 score

RateViz - Visualizations for instantaneous rate matrices

This package uses an instantaneous rate matrix (such as is used for models of DNA evolution, morphological character change over evolutionary history, and other areas) and summarizes it in various ways. These could include bubble plots, a network showing transitions, or calculations to figure out likely paths between two states.

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1.00 score 1 stars 6 scripts