CITATION_NOTICE.md

If you use lsaBGC-Pan, please cite the original lsaBGC study: https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000988

lsaBGC-Pan is made possible by many other tools including:

• BGC prediction software (can vary but please cite appropriately):

  • antiSMASH: https://academic.oup.com/nar/article/49/W1/W29/6274535
  • GECCO: https://www.biorxiv.org/content/10.1101/2021.05.03.442509v1

• Ortholog group identification:

  • OrthoFinder2: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1832-y
  • Panaroo: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02090-4

• General processing of sequencing data and phylogenies:

  • biopython: https://academic.oup.com/bioinformatics/article/25/11/1422/330687
  • ete3: https://academic.oup.com/mbe/article/33/6/1635/2579822

• Gene calling:

  • prodigal: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-119
  • pyrodigal: https://joss.theoj.org/papers/10.21105/joss.04296

• Visualization software:

  • ggplot2: https://ggplot2-book.org/
  • ggtree: https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12628
  • gggeenes: https://github.com/wilkox/gggenes
  • cowplot: https://wilkelab.org/cowplot/articles/plot_grid.html
  • iTol: https://pubmed.ncbi.nlm.nih.gov/30931475/

• GCF clustering and population-genetics analysis:

  • zol: https://www.biorxiv.org/content/10.1101/2023.06.07.544063v2
  • DIAMOND: https://www.nature.com/articles/nmeth.3176
  • MUSCLE5: https://www.nature.com/articles/s41467-022-34630-w

• Orthogroup to orthogroup and GCF to GCF (dis-)association analysis:

  • pyseer: https://academic.oup.com/bioinformatics/article/34/24/4310/5047751

• Annotation databases (from zol):

  • KOfam HMMs: https://academic.oup.com/bioinformatics/article/36/7/2251/5631907
  • PGAP HMMs: https://pubmed.ncbi.nlm.nih.gov/27342282/
  • MIBiG DB: https://academic.oup.com/nar/article/51/D1/D603/6833236
  • CARD: https://academic.oup.com/nar/article/51/D1/D690/6764414
  • Pfam DB: https://academic.oup.com/nar/article/49/D1/D412/5943818?login=false
  • ISFinder DB: https://academic.oup.com/nar/article/34/suppl_1/D32/1132247?login=false