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ConSpeciFix: classifying prokaryotic species based on gene flow.
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DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication.
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HyDe: A Python Package for Genome-Scale Hybridization Detection.
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Rabifier2: an improved bioinformatic classifier of Rab GTPases.
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PHYLUCE is a software package for the analysis of conserved genomic loci.
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pyNBS: a Python implementation for network-based stratification of tumor mutations.
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ICBdocker: a Docker image for proteome annotation and visualization.
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GeneSpy, a user-friendly and flexible genomic context visualizer.
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引用本文的文献

3
Co-evolution and Gene Transfers Drive Speciation Patterns in Host-Associated Bacteria.
Mol Biol Evol. 2024 Dec 6;41(12). doi: 10.1093/molbev/msae256.
4
Evolution of homologous recombination rates across bacteria.
Proc Natl Acad Sci U S A. 2024 Apr 30;121(18):e2316302121. doi: 10.1073/pnas.2316302121. Epub 2024 Apr 24.
6
Gene flow and species boundaries of the genus .
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Escherichia Coli: What Is and Which Are?
Mol Biol Evol. 2023 Jan 4;40(1). doi: 10.1093/molbev/msac273.
8
Gene flow and introgression are pervasive forces shaping the evolution of bacterial species.
Genome Biol. 2022 Nov 10;23(1):239. doi: 10.1186/s13059-022-02809-5.
9
Coastal Transient Niches Shape the Microdiversity Pattern of a Bacterioplankton Population with Reduced Genomes.
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10
Species divergence in gut-restricted bacteria of social bees.
Proc Natl Acad Sci U S A. 2022 May 3;119(18):e2115013119. doi: 10.1073/pnas.2115013119. Epub 2022 Apr 25.

本文引用的文献

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Pangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of spp.
Front Microbiol. 2018 Mar 12;9:428. doi: 10.3389/fmicb.2018.00428. eCollection 2018.
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Biological species are universal across Life's domains.
Genome Biol Evol. 2017 Feb 10;9(3):491-501. doi: 10.1093/gbe/evx026.
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Microbial Speciation.
Cold Spring Harb Perspect Biol. 2015 Sep 9;7(10):a018143. doi: 10.1101/cshperspect.a018143.
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The two-domain tree of life is linked to a new root for the Archaea.
Proc Natl Acad Sci U S A. 2015 May 26;112(21):6670-5. doi: 10.1073/pnas.1420858112. Epub 2015 May 11.
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Search and clustering orders of magnitude faster than BLAST.
Bioinformatics. 2010 Oct 1;26(19):2460-1. doi: 10.1093/bioinformatics/btq461. Epub 2010 Aug 12.
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A comparison of homologous recombination rates in bacteria and archaea.
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RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.
Bioinformatics. 2006 Nov 1;22(21):2688-90. doi: 10.1093/bioinformatics/btl446. Epub 2006 Aug 23.
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Genomic insights that advance the species definition for prokaryotes.
Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2567-72. doi: 10.1073/pnas.0409727102. Epub 2005 Feb 8.

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