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phylotaR: An Automated Pipeline for Retrieving Orthologous DNA Sequences from GenBank in R
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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A roadmap for global synthesis of the plant tree of life
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Reconstructing the evolutionary history of the Lorisidae using morphological, molecular, and geological data
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ggplot2: Elegant Graphics for Data Analysis
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Comparison of phylogenetic trees
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1038/nmeth.3176openalex-snapshot
Fast and sensitive protein alignment using DIAMOND
inferredcites →https://doi.org/10.1073/pnas.85.8.2444openalex-snapshot
Improved tools for biological sequence comparison.
inferredcites →https://doi.org/10.1080/10635150802158688openalex-snapshot
The PhyLoTA Browser: Processing GenBank for Molecular Phylogenetics Research
inferredcites →https://doi.org/10.1093/bioinformatics/btq461openalex-snapshot
Search and clustering orders of magnitude faster than BLAST
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
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Coalescent-Based Analyses of Genomic Sequence Data Provide a Robust Resolution of Phylogenetic Relationships among Major Groups of Gibbons
inferredcites →https://doi.org/10.1093/nar/gkq930openalex-snapshot
OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011
inferredcites →https://doi.org/10.1093/nar/gkx1019openalex-snapshot
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces
inferredcites →https://doi.org/10.1093/sysbio/45.3.323openalex-snapshot
The Triples Distance for Rooted Bifurcating Phylogenetic Trees
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Complete Generic-Level Phylogenetic Analyses of Palms (Arecaceae) with Comparisons of Supertree and Supermatrix Approaches
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Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa
inferredcites →https://doi.org/10.1101/gr.229202openalex-snapshot
BLAT —The BLAST -Like Alignment Tool
inferredcites →https://doi.org/10.1111/2041-210x.12055openalex-snapshot
phyloGenerator: an automated phylogeny generation tool for ecologists
inferredcites →https://doi.org/10.1111/j.1096-0031.1991.tb00045.xopenalex-snapshot
CONCEPTS AND TESTS OF HOMOLOGY IN THE CLADISTIC PARADIGM
inferredcites →https://doi.org/10.1128/aem.71.12.7724-7736.2005openalex-snapshot
At Least 1 in 20 16S rRNA Sequence Records Currently Held in Public Repositories Is Estimated To Contain Substantial Anomalies
inferredcites →https://doi.org/10.1186/1471-2105-10-329openalex-snapshot
PLAST: parallel local alignment search tool for database comparison
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Phylogenetic position of the langur genera Semnopithecus and Trachypithecus among Asian colobines, and genus affiliations of their species groups
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Origin and global diversification patterns of tropical rain forests: inferences from a complete genus-level phylogeny of palms
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treeman: an R package for efficient and intuitive manipulation of phylogenetic trees
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A Molecular Phylogeny of Living Primates
inferredcites →https://doi.org/10.32614/cran.package.devtoolsopenalex-snapshot
devtools: Tools to Make Developing R Packages Easier
inferredcites →https://doi.org/10.32614/cran.package.treemapifyopenalex-snapshot
treemapify: Draw Treemaps in 'ggplot2'
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unix: POSIX System Utilities
inferredcites →https://doi.org/10.32614/cran.package.xmlopenalex-snapshot
XML: Tools for Parsing and Generating XML Within R and S-Plus
inferredcites →https://doi.org/10.3390/life8020020openalex-snapshot
phylotaR: An Automated Pipeline for Retrieving Orthologous DNA Sequences from GenBank in R
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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DNA barcoding reveals different cestode helminth species in northern European marine and freshwater ringed seals
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inferred← citeshttps://doi.org/10.5852/ejt.2024.921.2429zenodo-depositor-declared
Integrating museum collections and molecules reveals genus-level synonymy and new species in red devil spiders (Araneae, Dysderidae) from the Middle East and Central Asia
inferred← citeshttps://doi.org/10.1002/ajb2.16330openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/ajb2.70166openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-3-032-09328-8_2openalex-snapshot
Phylogeny and Divergence Time Estimates of Neotropical Freshwater Fishes
inferred← citeshttps://doi.org/10.1007/s00239-026-10319-2openalex-snapshot
User Guided Selection and Alignment of Sequence Data by GeneMatrix
inferred← citeshttps://doi.org/10.1016/j.biocon.2022.109677openalex-snapshot
Spatial patterns of evolutionary diversity in Cactaceae show low ecological representation within protected areas
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Evolutionary signatures of a trade-off in direct and indirect defenses across the wild grape genus, Vitis
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Redefining Possible: Combining Phylogenomic and Supersparse Data in Frogs
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Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses?
inferred← citeshttps://doi.org/10.1093/zoolinnean/zlaa089openalex-snapshot
Integrative taxonomic revision of the woodlouse-hunter spider genusDysdera(Araneae: Dysderidae) in the Madeira archipelago with notes on its conservation status
inferred← citeshttps://doi.org/10.1093/zoolinnean/zlae068openalex-snapshot
Evolution of spider- and ant-eating habits in crab spiders (Araneae: Thomisidae)
inferred← citeshttps://doi.org/10.1098/rspb.2021.1199openalex-snapshot
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Alternative pathways into the deep sea: patterns in Bivalvia
inferred← citeshttps://doi.org/10.1101/2020.12.21.394551openalex-snapshot
PhylUp: phylogenetic alignment building with custom taxon sampling
inferred← citeshttps://doi.org/10.1101/2022.09.20.508664openalex-snapshot
Climate influences bill shape diversification in cavity-excavating birds
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The ‘phruta’ R package and ‘salphycon’ shiny app: increasing access, reproducibility, and transparency in phylogenetic analyses
inferred← citeshttps://doi.org/10.1101/2024.08.20.608795openalex-snapshot
Analysis of the effects of mating systems on lineage diversification across multiple genera
inferred← citeshttps://doi.org/10.1101/538728openalex-snapshot
SuperCRUNCH: A bioinformatics toolkit for creating and manipulating supermatrices and other large phylogenetic datasets
inferred← citeshttps://doi.org/10.1111/2041-210x.13392openalex-snapshot
SuperCRUNCH: A bioinformatics toolkit for creating and manipulating supermatrices and other large phylogenetic datasets
inferred← citeshttps://doi.org/10.1111/2041-210x.14147openalex-snapshot
The phruta r package: Increasing access, reproducibility and transparency in phylogenetic analyses
inferred← citeshttps://doi.org/10.1111/jse.13155openalex-snapshot
PyNCBIminer: A platform for assembling phylogenetic data sets via GenBank datamining
inferred← citeshttps://doi.org/10.11594/jtls.12.03.04openalex-snapshot
Reconstructing Phylogenies of Alocasia spp. (Araceae) Distributed in Indonesia for Conservation Prioritization
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Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life
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Phylogenetic revision of Gymnotidae (Teleostei: Gymnotiformes), with descriptions of six subgenera
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Datataxa: a new script to extract metadata sequence information from GenBank, the Flora of Bajío as a case study
inferred← citeshttps://doi.org/10.17129/botsci.3061openalex-snapshot
The Mexican flora as a case study in systematics: a meta-analysis of GenBank accessions
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restez: Create and Query a Local Copy of GenBank in R
inferred← citeshttps://doi.org/10.3389/fbinf.2024.1433995openalex-snapshot
Time-calibrated phylogeny of neotropical freshwater fishes
inferred← citeshttps://doi.org/10.3389/fpls.2022.909768openalex-snapshot
An open and continuously updated fern tree of life
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Building a Robust, Densely-Sampled Spider Tree of Life for Ecosystem Research
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Genome sequencing reveals extraordinary cephalic horns in the Madagascan dung beetle genus Helictopleurus (Coleoptera, Scarabaeinae): insight from a revision of fungicola species group
inferred← citeshttps://doi.org/10.59350/4h664-t9k57openalex-snapshot
phylotaR: Retrieve Orthologous Sequences from GenBank
inferred← citeshttps://doi.org/10.59350/6sym9-59x52openalex-snapshot
phylotaR: Retrieve Orthologous Sequences from GenBank
inferred← citeshttps://doi.org/10.7717/peerj.21681openalex-snapshot
Synthesis of molecular data on Mactroidea (Bivalvia): phylogenetic implications and open questions
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