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SuperCRUNCH: A bioinformatics toolkit for creating and manipulating supermatrices and other large phylogenetic datasets
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/cpbi.5openalex-snapshot
The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses
inferredcites →https://doi.org/10.1016/j.tree.2006.10.002openalex-snapshot
The supermatrix approach to systematics
inferredcites →https://doi.org/10.1016/j.ympev.2011.12.007openalex-snapshot
Applications of next-generation sequencing to phylogeography and phylogenetics
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1038/msb.2011.75openalex-snapshot
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
inferredcites →https://doi.org/10.1080/10635150802158688openalex-snapshot
The PhyLoTA Browser: Processing GenBank for Molecular Phylogenetics Research
inferredcites →https://doi.org/10.1089/cmb.2014.0156openalex-snapshot
PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences
inferredcites →https://doi.org/10.1093/bioinformatics/18.3.440openalex-snapshot
PatternHunter: faster and more sensitive homology search
inferredcites →https://doi.org/10.1093/bioinformatics/btl158openalex-snapshot
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btp348openalex-snapshot
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
inferredcites →https://doi.org/10.1093/bioinformatics/btv646openalex-snapshot
PHYLUCE is a software package for the analysis of conserved genomic loci
inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/molbev/msy159openalex-snapshot
MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons
inferredcites →https://doi.org/10.1093/nar/gkf436openalex-snapshot
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
inferredcites →https://doi.org/10.1093/sysbio/syr095openalex-snapshot
SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees
inferredcites →https://doi.org/10.1093/sysbio/syv033openalex-snapshot
Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference
inferredcites →https://doi.org/10.1093/sysbio/syw066openalex-snapshot
Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa
inferredcites →https://doi.org/10.1111/2041-210x.12055openalex-snapshot
phyloGenerator: an automated phylogeny generation tool for ecologists
inferredcites →https://doi.org/10.1111/2041-210x.13096openalex-snapshot
Py PHLAWD : A python tool for phylogenetic dataset construction
inferredcites →https://doi.org/10.1111/j.1365-313x.2006.02842.xopenalex-snapshot
Ethylene‐induced stomatal closure in Arabidopsis occurs via AtrbohF‐mediated hydrogen peroxide synthesis
inferredcites →https://doi.org/10.1111/mec.13108openalex-snapshot
The evolution of phylogeographic data sets
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/1471-2148-9-37openalex-snapshot
Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches
inferredcites →https://doi.org/10.1186/s13059-015-0688-zopenalex-snapshot
Ultra-large alignments using phylogeny-aware profiles
inferredcites →https://doi.org/10.12688/f1000research.2-191.v1openalex-snapshot
taxize: taxonomic search and retrieval in R
inferredcites →https://doi.org/10.32614/cran.package.taxizeopenalex-snapshot
taxize: Taxonomic Information from Around the Web
inferredcites →https://doi.org/10.3390/life8020020openalex-snapshot
phylotaR: An Automated Pipeline for Retrieving Orthologous DNA Sequences from GenBank in R
inferredcites →https://doi.org/10.3897/bdj.4.e8080openalex-snapshot
Challenges with using names to link digital biodiversity information
inferredcites →https://doi.org/10.4137/ebo.s35384openalex-snapshot
SUMAC: Constructing Phylogenetic Supermatrices and Assessing Partially Decisive Taxon Coverage
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.11646/zootaxa.5174.3.1zenodo-depositor-declared
Systematics of the Central African Spiny Reed Frog Afrixalus laevis (Anura: Hyperoliidae), with the description of two new species from the Albertine Rift
inferred← citeshttps://doi.org/10.1002/ece3.71380openalex-snapshot
Why the Long “Horns”? Fine‐Scale Morphology Suggests Tactile Demands Contributed to the Exaggeration of Male Longhorned Beetle Antennae (Coleoptera: Cerambycidae)
inferred← citeshttps://doi.org/10.1016/b978-0-443-31406-3.00012-6openalex-snapshot
Molecular phylogenetics for gaining insights into the evolution of forest communities
inferred← citeshttps://doi.org/10.1016/j.ympev.2023.107907openalex-snapshot
Frog phylogeny: A time-calibrated, species-level tree based on hundreds of loci and 5,242 species
inferred← citeshttps://doi.org/10.1016/j.ympev.2024.108272openalex-snapshot
A time-calibrated salamander phylogeny including 765 species and 503 genes
inferred← citeshttps://doi.org/10.1038/s41467-025-56820-yopenalex-snapshot
Negative global-scale association between genetic diversity and speciation rates in mammals
inferred← citeshttps://doi.org/10.1073/pnas.2514344122openalex-snapshot
When islands collide: Divergence predicts outcomes of secondary contact during the fusion of Sulawesi’s paleo-archipelago
inferred← citeshttps://doi.org/10.1080/12298093.2022.2116816openalex-snapshot
Re-Identification on Korean Penicillium Sequences in GenBank Collected by Software GenMine
inferred← citeshttps://doi.org/10.1093/aob/mcad153openalex-snapshot
Unravelling phylogenetic relationships of the tribe Cereeae using target enrichment sequencing
inferred← citeshttps://doi.org/10.1093/biolinnean/blaf027openalex-snapshot
Hidden barriers and phylogeographical divergence in the central Cerrado: a comparative and predictive analysis
inferred← citeshttps://doi.org/10.1093/evolut/qpad034openalex-snapshot
Selection on an extreme-yet-conserved larval life-history strategy in a tapeworm
inferred← citeshttps://doi.org/10.1093/jmammal/gyaf065openalex-snapshot
The genetic implications of translocations on Fisher ( Pekania pennanti ) populations in Montana and Idaho
inferred← citeshttps://doi.org/10.1093/sysbio/syaa064openalex-snapshot
Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses?
inferred← citeshttps://doi.org/10.1093/sysbio/syad026openalex-snapshot
Hybridization and Transgressive Evolution Generate Diversity in an Adaptive Radiation ofAnolisLizards
inferred← citeshttps://doi.org/10.1093/sysbio/syaf088openalex-snapshot
The Evolutionary History of Dragon Lizards (Squamata: Agamidae) Revealed by Phylogenomics
inferred← citeshttps://doi.org/10.1098/rspb.2025.2002openalex-snapshot
Alternative pathways into the deep sea: patterns in Bivalvia
inferred← citeshttps://doi.org/10.1101/2020.10.02.324277openalex-snapshot
Decolonizing Psocopteran Systematics: Holarctic Lineages Cannot Inform Diversity and Evolution in Tropics
inferred← citeshttps://doi.org/10.1101/2020.12.21.394551openalex-snapshot
PhylUp: phylogenetic alignment building with custom taxon sampling
inferred← citeshttps://doi.org/10.1101/2023.01.11.523621openalex-snapshot
The ‘phruta’ R package and ‘salphycon’ shiny app: increasing access, reproducibility, and transparency in phylogenetic analyses
inferred← citeshttps://doi.org/10.1101/2023.09.10.556973openalex-snapshot
The Origin And Speciation Of Orchids
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/10.1111/mec.70125openalex-snapshot
Wolbachia Host Shifts and Widespread Occurrence of Reproductive Manipulation Loci in European Butterflies
inferred← citeshttps://doi.org/10.1111/nph.19580openalex-snapshot
The origin and speciation of orchids
inferred← citeshttps://doi.org/10.1126/science.adh2449openalex-snapshot
The macroevolutionary singularity of snakes
inferred← citeshttps://doi.org/10.1163/1876312x-bja10055openalex-snapshot
Holarctic Lineages Cannot Inform Diversity and Evolution in the Neotropics – the barklice family Psocidae as a case study
inferred← citeshttps://doi.org/10.1186/s12864-025-11542-9openalex-snapshot
A conserved terpene cyclase gene in Sanghuangporus for abscisic acid-related sesquiterpenoid biosynthesis
inferred← citeshttps://doi.org/10.1186/s40168-025-02329-xopenalex-snapshot
Functionally distinct core microbes of Tricholoma matsutake revealed by cross-study analysis
inferred← citeshttps://doi.org/10.22215/etd/2020-14165openalex-snapshot
Population Genetics of Antimicrobial Resistance in Campylobacter isolates from across Canada
inferred← citeshttps://doi.org/10.3389/fevo.2021.630207openalex-snapshot
Museum Genomics Illuminate the High Specificity of a Bioluminescent Symbiosis for a Genus of Reef Fish
inferred← citeshttps://doi.org/10.3389/fpls.2022.909768openalex-snapshot
An open and continuously updated fern tree of life
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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