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SuperCRUNCH: A bioinformatics toolkit for creating and manipulating supermatrices and other large phylogenetic datasets

https://doi.org/10.1101/538728
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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/10.1080/10635150500541730openalex-snapshot
Multiple Sequence Alignment Accuracy and Phylogenetic Inference
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/molbev/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/molbev/msw046openalex-snapshot
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
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/nar/gkh340openalex-snapshot
MUSCLE: multiple sequence alignment with high accuracy and high throughput
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/sys004openalex-snapshot
Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales
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/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/10.1371/journal.pone.0018093openalex-snapshot
A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives
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.4852.2.6zenodo-depositor-declared
Goniurosaurus gezhi sp. nov., a new gecko species from Guangxi, China (Squamata: Eublepharidae)
inferred← citeshttps://doi.org/10.1007/s10531-020-01986-8openalex-snapshot
Species IUCN threat status level increases with elevation: a phylogenetic approach for Neotropical tree frog conservation
inferred← citeshttps://doi.org/10.1111/jse.12646openalex-snapshot
Biogeography and ecological niche evolution in Diapensiaceae inferred from phylogenetic analysis
inferred← citeshttps://doi.org/10.22215/etd/2019-13815openalex-snapshot
Genome-wide association study of Pseudomonas aeruginosa adaptations to the cystic fibrosis lung
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