Showing 54 of total 54 results (show query)
rsetienne
DAISIE:Dynamical Assembly of Islands by Speciation, Immigration and Extinction
Simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction. See Valente et al. (2015) <doi:10.1111/ele.12461>.
Maintained by Rampal S. Etienne. Last updated 1 months ago.
42.2 match 9 stars 8.59 score 55 scripts 1 dependents
danlwarren
ENMTools:Analysis of Niche Evolution using Niche and Distribution Models
Constructing niche models and analyzing patterns of niche evolution. Acts as an interface for many popular modeling algorithms, and allows users to conduct Monte Carlo tests to address basic questions in evolutionary ecology and biogeography. Warren, D.L., R.E. Glor, and M. Turelli (2008) <doi:10.1111/j.1558-5646.2008.00482.x> Glor, R.E., and D.L. Warren (2011) <doi:10.1111/j.1558-5646.2010.01177.x> Warren, D.L., R.E. Glor, and M. Turelli (2010) <doi:10.1111/j.1600-0587.2009.06142.x> Cardillo, M., and D.L. Warren (2016) <doi:10.1111/geb.12455> D.L. Warren, L.J. Beaumont, R. Dinnage, and J.B. Baumgartner (2019) <doi:10.1111/ecog.03900>.
Maintained by Dan Warren. Last updated 2 months ago.
19.9 match 105 stars 6.91 score 126 scripts
paternogbc
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).
Maintained by Gustavo Paterno. Last updated 5 years ago.
comparative-methodsecologyevolutionphylogeneticssensitivity-analysis
18.8 match 13 stars 6.38 score 61 scripts
joshwlambert
DAISIEprep:Extracts Phylogenetic Island Community Data from Phylogenetic Trees
Extracts colonisation and branching times of island species to be used for analysis in the R package 'DAISIE'. It uses phylogenetic and endemicity data to extract the separate island colonists and store them.
Maintained by Joshua W. Lambert. Last updated 1 months ago.
data-scienceisland-biogeographyphylogenetics
17.6 match 6 stars 6.78 score 24 scripts
tiago-simoes
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>.
Maintained by Tiago Simoes. Last updated 2 years ago.
20.0 match 4 stars 5.66 score 19 scripts
emmanuelparadis
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) whose results are returned into R.
Maintained by Emmanuel Paradis. Last updated 16 hours ago.
6.5 match 64 stars 17.22 score 13k scripts 599 dependents
pasraia
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.
Maintained by Silvia Castiglione. Last updated 7 months ago.
14.6 match 10 stars 7.48 score 83 scripts
richfitz
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.
Maintained by Richard G. FitzJohn. Last updated 6 months ago.
10.8 match 33 stars 8.51 score 524 scripts 4 dependents
abichat
yatah:Yet Another TAxonomy Handler
Provides functions to manage taxonomy when lineages are described with strings and ranks separated with special patterns like "|*__" or ";*__".
Maintained by Antoine Bichat. Last updated 11 months ago.
17.4 match 6 stars 4.65 score 15 scripts
davidorme
caper:Comparative Analyses of Phylogenetics and Evolution in R
Functions for performing phylogenetic comparative analyses.
Maintained by David Orme. Last updated 1 years ago.
10.1 match 1 stars 7.41 score 928 scripts 5 dependents
danlwarren
rwty:R We There Yet? Visualizing MCMC Convergence in Phylogenetics
Implements various tests, visualizations, and metrics for diagnosing convergence of MCMC chains in phylogenetics. It implements and automates many of the functions of the AWTY package in the R environment, as well as a host of other functions. Warren, Geneva, and Lanfear (2017), <doi:10.1093/molbev/msw279>.
Maintained by Dan Warren. Last updated 4 years ago.
9.6 match 30 stars 7.32 score 117 scriptsrsetienne
DDD:Diversity-Dependent Diversification
Implements maximum likelihood and bootstrap methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent, under various models including various types of key innovations. See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, <DOI:10.1098/rspb.2011.1439>, Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, <DOI:10.1086/667574>, Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099, <DOI:10.1111/2041-210X.12565> and Laudanno et al. 2021. Syst. Biol. 70: 389–407, <DOI:10.1093/sysbio/syaa048>. Also contains functions to simulate the diversity-dependent process.
Maintained by Rampal S. Etienne. Last updated 4 months ago.
7.4 match 4 stars 7.10 score 80 scripts 7 dependents
yhenryli
PAC:Partition-Assisted Clustering and Multiple Alignments of Networks
Implements partition-assisted clustering and multiple alignments of networks. It 1) utilizes partition-assisted clustering to find robust and accurate clusters and 2) discovers coherent relationships of clusters across multiple samples. It is particularly useful for analyzing single-cell data set. Please see Li et al. (2017) <doi:10.1371/journal.pcbi.1005875> for detail method description.
Maintained by Ye Henry Li. Last updated 4 years ago.
15.5 match 3.30 score 7 scripts
bioc
MicrobiotaProcess:A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework
MicrobiotaProcess is an R package for analysis, visualization and biomarker discovery of microbial datasets. It introduces MPSE class, this make it more interoperable with the existing computing ecosystem. Moreover, it introduces a tidy microbiome data structure paradigm and analysis grammar. It provides a wide variety of microbiome data analysis procedures under the unified and common framework (tidy-like framework).
Maintained by Shuangbin Xu. Last updated 5 months ago.
visualizationmicrobiomesoftwaremultiplecomparisonfeatureextractionmicrobiome-analysismicrobiome-data
5.1 match 183 stars 9.70 score 126 scripts 1 dependents
klausvigo
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).
Maintained by Klaus Schliep. Last updated 1 months ago.
softwaretechnologyqualitycontrolphylogenetic-analysisphylogeneticsopenblascpp
1.9 match 206 stars 16.69 score 2.5k scripts 135 dependents
brpetrucci
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>.
Maintained by Bruno do Rosario Petrucci. Last updated 1 months ago.
evolutionmacroevolutionpaleobiologypaleontologyphylogenetics
6.0 match 6 stars 4.95 score 4 scripts
cran
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.
Maintained by Christoph Heibl. Last updated 11 months ago.
6.4 match 4.28 score 128 scripts 1 dependents
thej022214
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>.
Maintained by Jeremy Beaulieu. Last updated 1 months ago.
3.0 match 6 stars 8.45 score 152 scripts
mkborregaard
nodiv:Compares the Distribution of Sister Clades Through a Phylogeny
An implementation of the nodiv algorithm, see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. <DOI:10.1111/2041-210X.12283>. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped.
Maintained by Michael Krabbe Borregaard. Last updated 2 years ago.
6.8 match 2 stars 3.45 score 28 scripts
ropensci
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.
Maintained by Shixiang Wang. Last updated 8 months ago.
blastngenbankpeer-reviewedphylogeneticssequence-alignment
4.0 match 23 stars 5.86 score 156 scripts
kbhoehn
dowser:B Cell Receptor Phylogenetics Toolkit
Provides a set of functions for inferring, visualizing, and analyzing B cell phylogenetic trees. Provides methods to 1) reconstruct unmutated ancestral sequences, 2) build B cell phylogenetic trees using multiple methods, 3) visualize trees with metadata at the tips, 4) reconstruct intermediate sequences, 5) detect biased ancestor-descendant relationships among metadata types Workflow examples available at documentation site (see URL). Citations: Hoehn et al (2022) <doi:10.1371/journal.pcbi.1009885>, Hoehn et al (2021) <doi:10.1101/2021.01.06.425648>.
Maintained by Kenneth Hoehn. Last updated 2 months ago.
3.4 match 6.81 score 84 scripts
skembel
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>.
Maintained by Steven W. Kembel. Last updated 2 years ago.
2.0 match 34 stars 11.42 score 1.1k scripts 16 dependents
ms609
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.
Maintained by Martin R. Smith. Last updated 1 months ago.
evolutionary-biologyphylogenetic-treesphylogeneticscpp
2.3 match 21 stars 9.92 score 124 scripts 10 dependents
cidm-ph
phylepic:Combined Visualisation of Phylogenetic and Epidemiological Data
A collection of utilities and 'ggplot2' extensions to assist with visualisations in genomic epidemiology. This includes the 'phylepic' chart, a visual combination of a phylogenetic tree and a matched epidemic curve. The included 'ggplot2' extensions such as date axes binned by week are relevant for other applications in epidemiology and beyond. The approach is described in Suster et al. (2024) <doi:10.1101/2024.04.02.24305229>.
Maintained by Carl Suster. Last updated 2 months ago.
genomicsgenomics-visualizationpublic-health
4.1 match 4.65 score 4 scriptsbioc
pepStat:Statistical analysis of peptide microarrays
Statistical analysis of peptide microarrays
Maintained by Gregory C Imholte. Last updated 5 months ago.
3.3 match 7 stars 5.62 score 4 scripts
lukejharmon
geiger:Analysis of Evolutionary Diversification
Methods for fitting macroevolutionary models to phylogenetic trees Pennell (2014) <doi:10.1093/bioinformatics/btu181>.
Maintained by Luke Harmon. Last updated 2 years ago.
2.3 match 1 stars 7.84 score 2.3k scripts 28 dependents
vanderleidebastiani
PCPS:Principal Coordinates of Phylogenetic Structure
Set of functions for analysis of Principal Coordinates of Phylogenetic Structure (PCPS).
Maintained by Vanderlei Julio Debastiani. Last updated 4 years ago.
4.5 match 1 stars 3.65 score 7 scriptsbioc
lefser:R implementation of the LEfSE method for microbiome biomarker discovery
lefser is the R implementation of the popular microbiome biomarker discovery too, LEfSe. It uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis to find biomarkers from two-level classes (and optional sub-classes).
Maintained by Sehyun Oh. Last updated 26 days ago.
softwaresequencingdifferentialexpressionmicrobiomestatisticalmethodclassificationbioconductor-package
1.9 match 55 stars 8.47 score 56 scripts
acorg
Racmacs:Antigenic Cartography Macros
A toolkit for making antigenic maps from immunological assay data, in order to quantify and visualize antigenic differences between different pathogen strains as described in Smith et al. (2004) <doi:10.1126/science.1097211> and used in the World Health Organization influenza vaccine strain selection process. Additional functions allow for the diagnostic evaluation of antigenic maps and an interactive viewer is provided to explore antigenic relationships amongst several strains and incorporate the visualization of associated genetic information.
Maintained by Sam Wilks. Last updated 9 months ago.
1.8 match 21 stars 8.06 score 362 scriptsropensci
phruta:Phylogenetic Reconstruction and Time-dating
The phruta R package is designed to simplify the basic phylogenetic pipeline. Specifically, all code is run within the same program and data from intermediate steps are saved in independent folders. Furthermore, all code is run within the same environment which increases the reproducibility of your analysis. phruta retrieves gene sequences, combines newly downloaded and local gene sequences, and performs sequence alignments.
Maintained by Cristian Roman Palacios. Last updated 8 months ago.
2.6 match 9 stars 4.75 score 14 scriptscran
BAMMtools:Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees
Provides functions for analyzing and visualizing complex macroevolutionary dynamics on phylogenetic trees. It is a companion package to the command line program BAMM (Bayesian Analysis of Macroevolutionary Mixtures) and is entirely oriented towards the analysis, interpretation, and visualization of evolutionary rates. Functionality includes visualization of rate shifts on phylogenies, estimating evolutionary rates through time, comparing posterior distributions of evolutionary rates across clades, comparing diversification models using Bayes factors, and more.
Maintained by Pascal Title. Last updated 6 months ago.
4.1 match 3.03 score 2 dependents
ms609
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.
Maintained by Martin R. Smith. Last updated 3 days ago.
bioinformaticsmorphological-analysisphylogeneticsresearch-tooltree-searchcpp
1.3 match 7 stars 7.89 score 51 scriptsabichat
scimo:Extra Recipes Steps for Dealing with Omics Data
Omics data (e.g. transcriptomics, proteomics, metagenomics...) offer a detailed and multi-dimensional perspective on the molecular components and interactions within complex biological (eco)systems. Analyzing these data requires adapted procedures, which are implemented as steps according to the 'recipes' package.
Maintained by Antoine BICHAT. Last updated 9 months ago.
1.9 match 4 stars 4.90 score 4 scripts
thibautjombart
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>.
Maintained by Michelle Kendall. Last updated 2 years ago.
1.2 match 28 stars 7.39 score 63 scriptsbioc
Pviz:Peptide Annotation and Data Visualization using Gviz
Pviz adapts the Gviz package for protein sequences and data.
Maintained by Renan Sauteraud. Last updated 5 months ago.
visualizationproteomicsmicroarray
1.8 match 4.48 score 4 scriptsropensci
treestartr:Generate Starting Trees For Combined Molecular, Morphological and Stratigraphic Data
Combine a list of taxa with a phylogeny to generate a starting tree for use in total evidence dating analyses.
Maintained by April Wright. Last updated 5 years ago.
1.8 match 9 stars 3.86 score 16 scriptscran
mvSLOUCH:Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses
Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history. See K. Bartoszek, J, Pienaar, P. Mostad, S. Andersson, T. F. Hansen (2012) <doi:10.1016/j.jtbi.2012.08.005>. The suggested PCMBaseCpp package (which significantly speeds up the likelihood calculations) can be obtained from <https://github.com/venelin/PCMBaseCpp/>.
Maintained by Krzysztof Bartoszek. Last updated 1 years ago.
1.8 match 3.00 score 1 dependents
theropod1
paleoDiv:Extracting and Visualizing Paleobiodiversity
Contains various tools for conveniently downloading and editing taxon-specific datasets from the Paleobiology Database <https://paleobiodb.org>, extracting information on abundance, temporal distribution of subtaxa and taxonomic diversity through deep time, and visualizing these data in relation to phylogeny and stratigraphy.
Maintained by Darius Nau. Last updated 5 months ago.
1.6 match 2 stars 2.78 scorecran
StrainRanking:Ranking of Pathogen Strains
Regression-based ranking of pathogen strains with respect to their contributions to natural epidemics, using demographic and genetic data sampled in the curse of the epidemics. This package also includes the GMCPIC test.
Maintained by Samuel Soubeyrand. Last updated 7 years ago.
3.6 match 1.00 score
amsibioinfo
phylometrics:Estimating Statistical Errors of Phylogenetic Metrics
Provides functions to estimate statistical errors of phylogenetic metrics particularly to detect binary trait influence on diversification, as well as a function to simulate trees with fixed number of sampled taxa and trait prevalence.
Maintained by Xia Hua. Last updated 9 years ago.
1.7 match 1.70 score 7 scripts
cobeylab
imprinting:Calculate Birth Year-Specific Probabilities of Immune Imprinting to Influenza
Reconstruct birth-year specific probabilities of immune imprinting to influenza A, using the methods of Gostic et al. (2016) <doi:10.1126/science.aag1322>. Plot, save, or export the calculated probabilities for use in your own research. By default, the package calculates subtype-specific imprinting probabilities, but with user-provided frequency data, it is possible to calculate probabilities for arbitrary kinds of primary exposure to influenza A, including primary vaccination and exposure to specific clades, strains, etc.
Maintained by Alex Byrnes. Last updated 2 years ago.
0.5 match 4.15 score 14 scripts
ashipunov
shipunov:Miscellaneous Functions from Alexey Shipunov
A collection of functions for data manipulation, plotting and statistical computing, to use separately or with the book "Visual Statistics. Use R!": Shipunov (2020) <http://ashipunov.info/shipunov/software/r/r-en.htm>. Dr Alexey Shipunov died in December 2022. Most useful functions: Bclust(), Jclust() and BootA() which bootstrap hierarchical clustering; Recode() which does multiple recoding in a fast, simple and flexible way; Misclass() which outputs confusion matrix even if classes are not concerted; Overlap() which measures group separation on any projection; Biarrows() which converts any scatterplot into biplot; and Pleiad() which is fast and flexible correlogram.
Maintained by ORPHANED. Last updated 2 years ago.
1.8 match 1.00 score 9 scripts
gregoryschwartz
TooManyCellsR:An R Wrapper for 'TooManyCells'
An R wrapper for using 'TooManyCells', a command line program for clustering, visualizing, and quantifying cell clade relationships. See <https://gregoryschwartz.github.io/too-many-cells/> for more details.
Maintained by Gregory W. Schwartz. Last updated 5 years ago.
0.5 match 25 stars 3.40 score 5 scriptscran
indelmiss:Insertion Deletion Analysis While Accounting for Possible Missing Data
Genome-wide gene insertion and deletion rates can be modelled in a maximum likelihood framework with the additional flexibility of modelling potential missing data using the models included within. These models simultaneously estimate insertion and deletion (indel) rates of gene families and proportions of "missing" data for (multiple) taxa of interest. The likelihood framework is utilized for parameter estimation. A phylogenetic tree of the taxa and gene presence/absence patterns (with data ordered by the tips of the tree) are required. See Dang et al. (2016) <doi:10.1534/genetics.116.191973> for more details.
Maintained by Utkarsh J. Dang. Last updated 2 years ago.
1.6 match 1.04 score 11 scriptsropensci
onekp:Retrieve Data from the 1000 Plants Initiative (1KP)
The 1000 Plants Initiative (www.onekp.com) has sequenced the transcriptomes of over 1000 plant species. This package allows these sequences and metadata to be retrieved and filtered by code, species or recursively by clade. Scientific names and NCBI taxonomy IDs are both supported.
Maintained by Dhakal Rijan. Last updated 2 years ago.
0.5 match 13 stars 2.81 score 4 scripts
timothystephens
PhySortR:A Fast, Flexible Tool for Sorting Phylogenetic Trees
Screens and sorts phylogenetic trees in both traditional and extended Newick format. Allows for the fast and flexible screening (within a tree) of Exclusive clades that comprise only the target taxa and/or Non- Exclusive clades that includes a defined portion of non-target taxa.
Maintained by Timothy Stephens. Last updated 1 months ago.
0.8 match 1 stars 1.48 score 2 scripts