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panX: pan-genome analysis and exploration

https://doi.org/10.1101/072082

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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/bies.201100062openalex-snapshot

Orthology prediction methods: A quality assessment using curated protein families

inferredcites →https://doi.org/10.1007/bf02101694openalex-snapshot

Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

inferredcites →https://doi.org/10.1016/j.mib.2008.09.006openalex-snapshot

Comparative genomics: the bacterial pan-genome

inferredcites →https://doi.org/10.1016/j.mib.2014.11.016openalex-snapshot

Ten years of pan-genome analyses

inferredcites →https://doi.org/10.1016/j.tig.2008.12.004openalex-snapshot

Estimating the size of the bacterial pan-genome

inferredcites →https://doi.org/10.1038/35012500openalex-snapshot

Lateral gene transfer and the nature of bacterial innovation

inferredcites →https://doi.org/10.1038/ismej.2014.211openalex-snapshot

Physiology and evolution of nitrate acquisition in Prochlorococcus

inferredcites →https://doi.org/10.1038/ncomms4956openalex-snapshot

Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus

inferredcites →https://doi.org/10.1038/nmeth.3176openalex-snapshot

Fast and sensitive protein alignment using DIAMOND

inferredcites →https://doi.org/10.1038/nmicrobiol.2016.41openalex-snapshot

Identifying lineage effects when controlling for population structure improves power in bacterial association studies

inferredcites →https://doi.org/10.1038/nrg3962openalex-snapshot

Horizontal gene transfer: building the web of life

inferredcites →https://doi.org/10.1038/nrmicro1234openalex-snapshot

Mechanisms of, and Barriers to, Horizontal Gene Transfer between Bacteria

inferredcites →https://doi.org/10.1038/nrmicro3378openalex-snapshot

Prochlorococcus: the structure and function of collective diversity

inferredcites →https://doi.org/10.1038/sdata.2014.34openalex-snapshot

Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus

inferredcites →https://doi.org/10.1038/sdata.2015.58openalex-snapshot

Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae

inferredcites →https://doi.org/10.1073/pnas.0401526101openalex-snapshot

Transfer of photosynthesis genes to and from Prochlorococcus viruses

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/14.1.68openalex-snapshot

SplitsTree: analyzing and visualizing evolutionary data.

inferredcites →https://doi.org/10.1093/bioinformatics/18.2.337openalex-snapshot

Generating samples under a Wright–Fisher neutral model of genetic variation

inferredcites →https://doi.org/10.1093/bioinformatics/bth198openalex-snapshot

Phylogenetic trees based on gene content

inferredcites →https://doi.org/10.1093/bioinformatics/btr655openalex-snapshot

PGAP: pan-genomes analysis pipeline

inferredcites →https://doi.org/10.1093/bioinformatics/btt100openalex-snapshot

BioJS: an open source JavaScript framework for biological data visualization

inferredcites →https://doi.org/10.1093/bioinformatics/btu017openalex-snapshot

PanGP: A tool for quickly analyzing bacterial pan-genome profile

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/bioinformatics/btu153openalex-snapshot

Prokka: rapid prokaryotic genome annotation

inferredcites →https://doi.org/10.1093/bioinformatics/btv381openalex-snapshot

nextflu: real-time tracking of seasonal influenza virus evolution in humans

inferredcites →https://doi.org/10.1093/bioinformatics/btv421openalex-snapshot

Roary: rapid large-scale prokaryote pan genome analysis

inferredcites →https://doi.org/10.1093/gbe/evs016openalex-snapshot

The Infinitely Many Genes Model for the Distributed Genome of Bacteria

inferredcites →https://doi.org/10.1093/molbev/msj030openalex-snapshot

Application of Phylogenetic Networks in Evolutionary Studies

inferredcites →https://doi.org/10.1093/molbev/msu088openalex-snapshot

Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads

inferredcites →https://doi.org/10.1093/molbev/msw062openalex-snapshot

Estimating the Frequency of Horizontal Gene Transfer Using Phylogenetic Models of Gene Gain and Loss

inferredcites →https://doi.org/10.1093/nar/30.7.1575openalex-snapshot

An efficient algorithm for large-scale detection of protein families

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/gks757openalex-snapshot

PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species

inferredcites →https://doi.org/10.1093/nar/gku1196openalex-snapshot

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

inferredcites →https://doi.org/10.1093/nar/gkv1070openalex-snapshot

KEGG as a reference resource for gene and protein annotation

inferredcites →https://doi.org/10.1101/gr.1224503openalex-snapshot

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

inferredcites →https://doi.org/10.1101/gr.147710.112openalex-snapshot

A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic

inferredcites →https://doi.org/10.1101/sqb.2009.74.006openalex-snapshot

The Phylogenetic Forest and the Quest for the Elusive Tree of Life

inferredcites →https://doi.org/10.1109/tvcg.2011.185openalex-snapshot

D³ Data-Driven Documents

inferredcites →https://doi.org/10.1111/j.1558-5646.1992.tb01991.xopenalex-snapshot

PHYLOGENIES FROM RESTRICTION SITES: A MAXIMUM‐LIKELIHOOD APPROACH

inferredcites →https://doi.org/10.1128/jb.01382-07openalex-snapshot

Evolution of Acetoclastic Methanogenesis in Methanosarcina via Horizontal Gene Transfer from Cellulolytic Clostridia

inferredcites →https://doi.org/10.1186/1471-2105-11-1openalex-snapshot

Detection of gene pathways with predictive power for breast cancer prognosis

inferredcites →https://doi.org/10.1186/1471-2105-11-461openalex-snapshot

Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions

inferredcites →https://doi.org/10.1186/s12859-015-0625-xopenalex-snapshot

Evaluation of BLAST-based edge-weighting metrics used for homology inference with the Markov Clustering algorithm

inferredcites →https://doi.org/10.1186/s12859-015-0690-1openalex-snapshot

Erratum to: Evaluation of BLAST-based edge-weighting metrics used for homology inference with the Markov Clustering algorithm

inferredcites →https://doi.org/10.1186/s12915-014-0066-4openalex-snapshot

Genomes in turmoil: Quantification of genome dynamics in prokaryote supergenomes

inferredcites →https://doi.org/10.1186/s13059-015-0721-2openalex-snapshot

OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy

inferredcites →https://doi.org/10.1186/s13059-015-0726-xopenalex-snapshot

Real-time digital pathogen surveillance — the time is now

inferredcites →https://doi.org/10.1214/09-aap657openalex-snapshot

The diversity of a distributed genome in bacterial populations

inferredcites →https://doi.org/10.1371/journal.pcbi.1004041openalex-snapshot

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

inferredcites →https://doi.org/10.1371/journal.pone.0009490openalex-snapshot

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

inferredcites →https://doi.org/10.1371/journal.pone.0088837openalex-snapshot

Strong Genome-Wide Selection Early in the Evolution of Prochlorococcus Resulted in a Reduced Genome through the Loss of a Large Number of Small Effect Genes

inferredcites →https://doi.org/10.1371/journal.pone.0092798openalex-snapshot

A Reference Pan-Genome Approach to Comparative Bacterial Genomics: Identification of Novel Epidemiological Markers in Pathogenic Campylobacter

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/978-3-030-38281-0_3openalex-snapshot

The Bacterial Guide to Designing a Diversified Gene Portfolio

inferred← citeshttps://doi.org/10.1007/978-3-319-89929-9_15openalex-snapshot

Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes

inferred← citeshttps://doi.org/10.1038/nmicrobiol.2017.40openalex-snapshot

Why prokaryotes have pangenomes

inferred← citeshttps://doi.org/10.1093/bioinformatics/btac308openalex-snapshot

ODGI: understanding pangenome graphs

inferred← citeshttps://doi.org/10.1093/femsec/fiy026openalex-snapshot

DNA stable-isotope probing identifies uncultivated members of Pseudonocardia associated with biodegradation of pyrene in agricultural soil

inferred← citeshttps://doi.org/10.1093/molbev/msz225openalex-snapshot

Fine-Scale Haplotype Structure Reveals Strong Signatures of Positive Selection in a Recombining Bacterial Pathogen

inferred← citeshttps://doi.org/10.1101/098392openalex-snapshot

BGDMdocker: a Docker workflow for analysis and visualization pan-genome and biosynthetic gene clusters of bacterial

inferred← citeshttps://doi.org/10.1101/2020.12.11.421487openalex-snapshot

The hidden pangenome: comparative genomics reveals pervasive diversity in symbiotic and free-living sulfur-oxidizing bacteria

inferred← citeshttps://doi.org/10.1101/2023.01.17.524402openalex-snapshot

Predicting Protein-encoding Gene Content in Escherichia coli Genomes

inferred← citeshttps://doi.org/10.1101/215707openalex-snapshot

Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes

inferred← citeshttps://doi.org/10.1128/iai.00211-19openalex-snapshot

Bacterial Microcompartment-Mediated Ethanolamine Metabolism in Escherichia coli Urinary Tract Infection

inferred← citeshttps://doi.org/10.1128/jcm.00480-18openalex-snapshot

Real-Time Analysis and Visualization of Pathogen Sequence Data

inferred← citeshttps://doi.org/10.1128/msystems.00701-22openalex-snapshot

Longitudinal, Multi-Platform Metagenomics Yields a High-Quality Genomic Catalog and Guides an In Vitro Model for Cheese Communities

inferred← citeshttps://doi.org/10.11606/d.95.2020.tde-17122019-223725openalex-snapshot

Genômica comparativa aplicada no estudo da invasividade de Streptococcus pyogenes

inferred← citeshttps://doi.org/10.11606/t.95.2019.tde-02032020-102628openalex-snapshot

GTACG: um arcabouço computacional focado em genômica comparativa de bactérias de um mesmo ramo evolutivo

inferred← citeshttps://doi.org/10.1186/s12859-018-2250-yopenalex-snapshot

PanACEA: a bioinformatics tool for the exploration and visualization of bacterial pan-chromosomes

inferred← citeshttps://doi.org/10.1186/s12859-020-03657-5openalex-snapshot

GenAPI: a tool for gene absence-presence identification in fragmented bacterial genome sequences

inferred← citeshttps://doi.org/10.1186/s12864-017-4337-7openalex-snapshot

PGAP-X: extension on pan-genome analysis pipeline

inferred← citeshttps://doi.org/10.1371/journal.pgen.1007763openalex-snapshot

Metabolic adaptations underlying genome flexibility in prokaryotes

inferred← citeshttps://doi.org/10.24072/pcjournal.415openalex-snapshot

Revisiting pangenome openness with k-mers

inferred← citeshttps://doi.org/10.3329/bjm.v35i2.42638openalex-snapshot

Potential Drug Target Identification of Legionella pneumophila by Subtractive Genome Analysis: An In Silico Approach

inferred← citeshttps://doi.org/10.3389/fmicb.2021.660920openalex-snapshot

Insights on the Evolutionary Genomics of the Blautia Genus: Potential New Species and Genetic Content Among Lineages

inferred← citeshttps://doi.org/10.7150/ijbs.58220openalex-snapshot

Gene Presence/Absence Variation analysis of coronavirus family displays its pan-genomic diversity

inferred← citeshttps://doi.org/10.7287/peerj.3948v0.1/reviews/1openalex-snapshot

Peer Review #1 of "BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters (v0.1)"

inferred← citeshttps://doi.org/10.7287/peerj.3948v0.1/reviews/2openalex-snapshot

Peer Review #2 of "BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters (v0.1)"

inferred← citeshttps://doi.org/10.7287/peerj.3948v0.2/reviews/2openalex-snapshot

Peer Review #2 of "BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters (v0.2)"

Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.