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Genesis and Gappa: Processing, Analyzing and Visualizing Phylogenetic (Placement) Data
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1006/jmbi.2000.4042openalex-snapshot
T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. Thornton
inferredcites →https://doi.org/10.1007/bf01734359openalex-snapshot
Evolutionary trees from DNA sequences: A maximum likelihood approach
inferredcites →https://doi.org/10.1038/s41559-017-0091openalex-snapshot
Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests
inferredcites →https://doi.org/10.1038/s41564-018-0156-0openalex-snapshot
Methods for phylogenetic analysis of microbiome data
inferredcites →https://doi.org/10.1073/pnas.85.8.2444openalex-snapshot
Improved tools for biological sequence comparison.
inferredcites →https://doi.org/10.1093/bioinformatics/13.3.235openalex-snapshot
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
inferredcites →https://doi.org/10.1093/bioinformatics/17.8.754openalex-snapshot
MRBAYES: Bayesian inference of phylogenetic trees
inferredcites →https://doi.org/10.1093/bioinformatics/btg412openalex-snapshot
APE: Analyses of Phylogenetics and Evolution in R language
inferredcites →https://doi.org/10.1093/bioinformatics/btp163openalex-snapshot
Biopython: freely available Python tools for computational molecular biology and bioinformatics
inferredcites →https://doi.org/10.1093/bioinformatics/btq228openalex-snapshot
DendroPy: a Python library for phylogenetic computing
inferredcites →https://doi.org/10.1093/bioinformatics/bty767openalex-snapshot
Methods for automatic reference trees and multilevel phylogenetic placement
inferredcites →https://doi.org/10.1093/molbev/msp098openalex-snapshot
INDELible: A Flexible Simulator of Biological Sequence Evolution
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/msx302openalex-snapshot
Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets
inferredcites →https://doi.org/10.1093/molbev/msy014openalex-snapshot
The State of Software for Evolutionary Biology
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/gkn741openalex-snapshot
Database resources of the National Center for Biotechnology Information
inferredcites →https://doi.org/10.1093/nar/gks1219openalex-snapshot
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
inferredcites →https://doi.org/10.1093/nar/gkt1209openalex-snapshot
The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks
inferredcites →https://doi.org/10.1093/nar/gkw290openalex-snapshot
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
inferredcites →https://doi.org/10.1093/nar/gkw396openalex-snapshot
Phylogeny-aware identification and correction of taxonomically mislabeled sequences
inferredcites →https://doi.org/10.1093/sysbio/syr010openalex-snapshot
Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood
inferredcites →https://doi.org/10.1093/sysbio/syy054openalex-snapshot
EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences
inferredcites →https://doi.org/10.1093/sysbio/syz058openalex-snapshot
Quartet-Based Computations of Internode Certainty Provide Robust Measures of Phylogenetic Incongruence
inferredcites →https://doi.org/10.1101/447110openalex-snapshot
RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference
inferredcites →https://doi.org/10.1111/2041-210x.12628openalex-snapshot
ggtree : an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data
inferredcites →https://doi.org/10.1111/j.1467-9868.2011.01018.xopenalex-snapshot
The Phylogenetic Kantorovich–Rubinstein Metric for Environmental Sequence Samples
inferredcites →https://doi.org/10.1137/0222017openalex-snapshot
Recursive Star-Tree Parallel Data Structure
inferredcites →https://doi.org/10.1186/1471-2105-11-538openalex-snapshot
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
inferredcites →https://doi.org/10.1371/journal.pone.0035495openalex-snapshot
Perceptions and Experiences of Research Participants on Gender-Based Violence Community Based Survey: Implications for Ethical Guidelines
inferredcites →https://doi.org/10.1371/journal.pone.0056859openalex-snapshot
Edge Principal Components and Squash Clustering: Using the Special Structure of Phylogenetic Placement Data for Sample Comparison
inferredcites →https://doi.org/10.1371/journal.pone.0217050openalex-snapshot
Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples
inferredcites →https://doi.org/10.3389/fgene.2015.00348openalex-snapshot
The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics
inferredcites →https://doi.org/10.4137/ebo.s19199openalex-snapshot
Evaluating the Accuracy and Efficiency of Multiple Sequence Alignment Methods
inferredcites →https://doi.org/10.7717/peerj.2969openalex-snapshot
Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1007/s00203-020-02165-7openalex-snapshot
Taxonomic and functional analyses reveal existence of virulence and antibiotic resistance genes in beach sand bacterial populations
inferred← citeshttps://doi.org/10.1007/s10661-020-08823-zopenalex-snapshot
Distribution and comparison of bacterial communities in HVAC systems of two university buildings: Implications for indoor air quality and public health
inferred← citeshttps://doi.org/10.1038/s41586-021-04332-2openalex-snapshot
Petabase-scale sequence alignment catalyses viral discovery
inferred← citeshttps://doi.org/10.1099/mgen.0.000463openalex-snapshot
Geographically structured genomic diversity of non-human primate-infecting Treponema pallidum subsp. pertenue
inferred← citeshttps://doi.org/10.1101/2021.11.01.466765openalex-snapshot
Global patterns and rates of habitat transitions across the eukaryotic tree of life
inferred← citeshttps://doi.org/10.1101/2022.10.02.510531openalex-snapshot
Celiac dysbiosis does not transcend geographic boundaries
inferred← citeshttps://doi.org/10.1101/2022.10.05.510990openalex-snapshot
Revaluation of old data with new techniques reveals novel insights into the celiac microbiome
inferred← citeshttps://doi.org/10.1101/2022.11.11.516104openalex-snapshot
Comparison of phylogenetic placements to pairwise alignments for taxonomic assignment of ciliate OTUs
inferred← citeshttps://doi.org/10.1111/1755-0998.13255openalex-snapshot
SCRAPP : A tool to assess the diversity of microbial samples from phylogenetic placements
inferred← citeshttps://doi.org/10.1186/s40168-020-00977-9openalex-snapshot
Seasonal shifts in the gut microbiome indicate plastic responses to diet in wild geladas
inferred← citeshttps://doi.org/10.70675/cbaa029bz2850z4b26z97e7z7c1db113c35bopenalex-snapshot
Structure and trophic diversity of picoeukaryotic primary producers across the global ocean
inferred← citeshttps://doi.org/10.70675/f0308064z2fe8z44fczb92dzb797ed7fe3edopenalex-snapshot
Metabarcoding and metagenomic approaches to decipher microbial communities in suboxic environments
inferred← citeshttps://doi.org/10.7717/peerj.12345openalex-snapshot
The inconsistent microbiota of Budu , the Malaysian fermented anchovy sauce, revealed through 16S amplicon sequencing
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