6. dependencies

Citations for dependencies, databases, and related software

Please consider citing the following accordingly!

• pyrodigal, prodigal, and miniprot for gene-calling/mapping.
  • Pyrodigal: Python bindings and interface to Prodigal, an efficient method for gene prediction in prokaryotes
  • Prodigal: prokaryotic gene recognition and translation initiation site identification
  • Protein-to-genome alignment with miniprot
• MUSCLE5 for performing multiple sequence alignments and PAL2NAL for converting to codon alignments.
  • Muscle5: High-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny
  • PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
• DIAMOND for alignments in determining ortholog groups and FastTree2 for subsequent phylogeny construction.
  • Fast and sensitive protein alignment using DIAMOND
  • FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
• CD-HIT for query protein clustering in fai and 're-inflation' approach in zol.
  • CD-HIT: accelerated for clustering the next-generation sequencing data
• HyPhy and FASTME for selection analyses.
  • HyPhy: hypothesis testing using phylogenies
  • GARD: a genetic algorithm for recombination detection
  • FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection
  • Gene-Wide Identification of Episodic Selection
  • FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program
• peptides.py for calculation of peptide property stats.
• skani for dereplication of gene-clusters/GenBanks.
  • Fast and robust metagenomic sequence comparison through sparse chaining with skani
• antiSMASH, GECCO, DeepBGC, geNomad, MOB-suite, PhiSpy, VIBRANT, or ICEfinder if you used to identify a BGC, phage, plasmids, or ICEs.
  • antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation
  • Accurate de novo identification of biosynthetic gene clusters with GECCO
  • A deep learning genome-mining strategy for biosynthetic gene cluster prediction
  • ICEberg 2.0: an updated database of bacterial integrative and conjugative elements
  • Identification of mobile genetic elements with geNomad
  • PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies
  • MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies
• PFAM, KEGG, NCBI's PGAP, MIBiG, VOG, MOB-suite, PaperBlast, VFDB, CARD, and ISFinder databases used for annotation.
  • Pfam: The protein families database in 2021
  • VOGDB—Database of Virus Orthologous Groups
  • KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold
  • RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation
  • MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters
  • PaperBLAST: Text Mining Papers for Information about Homologs
  • VFDB 2022: a general classification scheme for bacterial virulence factors
  • CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database
  • ISfinder: the reference centre for bacterial insertion sequences
  • MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies
• GToTree and the study by Hug et al. 2016 for identification of universally conserved ribosomal proteins.
  • A new view of the tree of life
  • GToTree: a user-friendly workflow for phylogenomics
• DIAMOND and PyHMMER for performing functional annotations against consensus ortholog group sequences in zol.
  • Fast and sensitive protein alignment using DIAMOND
  • PyHMMER: a Python library binding to HMMER for efficient sequence analysis
• lsaBGC, BiG-SCAPE/CORASON, cblaster/CAGECAT, BiG-SLICE, vConTACT v2.0, or IslandCompare studies if you used them to identify homologous gene clusters.
  • Evolutionary investigations of the biosynthetic diversity in the skin microbiome using lsaBGC
  • A computational framework to explore large-scale biosynthetic diversity
  • cblaster: a remote search tool for rapid identification and visualization of homologous gene clusters
  • CAGECAT: The CompArative GEne Cluster Analysis Toolbox for rapid search and visualisation of homologous gene clusters
  • BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters
  • Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks
  • Enabling genomic island prediction and comparison in multiple genomes to investigate bacterial evolution and outbreaks
• gravis for interactive network visualization framework used in cgcg
  • Interactive graph visualizations with Python and HTML/CSS/JS.