zDB: bacterial comparative genomics made easy Marquis, Bastian and Pillonel, Trestan and Carrara, Alessia and Bertelli, Claire, mSystems, 9(7):e00473--24, 2024 (Pubmed)
Other references
High-throughput sequencing and clinical microbiology: progress, opportunities and challenges. Pallen, Mark J and Loman, Nicholas J and Penn, Charles W, Current opinion in microbiology, 13(5):625--31, 2010 (Pubmed)
UniProt: the universal protein knowledgebase UniProt Consortium and others, Nucleic acids research, 46(5):2699, 2018 (Pubmed)
BlasterJS: A novel interactive JavaScript visualisation component for BLAST alignment results Blanco-M{\'\i}guez, Aitor and Fdez-Riverola, Florentino and S{\'a}nchez, Borja and Louren{\c{c}}o, An{\'a}lia, PLoS One, 13(10):e0205286, 2018 (Pubmed)
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Parks, Donovan H and Imelfort, Michael and Skennerton, Connor T and Hugenholtz, Philip and Tyson, Gene W, Genome research, 25(7):1043--1055, 2015 (Pubmed)
Basic local alignment search tool Altschul, Stephen F and Gish, Warren and Miller, Webb and Myers, Eugene W and Lipman, David J, Journal of molecular biology, 215(3):403--410, 1990 (Pubmed)
CDD/SPARCLE: the conserved domain database in 2020 Lu, Shennan and Wang, Jiyao and Chitsaz, Farideh and Derbyshire, Myra K and Geer, Renata C and Gonzales, Noreen R and Gwadz, Marc and Hurwitz, David I and Marchler, Gabriele H and Song, James S and others, Nucleic acids research, 48(D1):D265--D268, 2020 (Pubmed)
KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold Aramaki, Takuya and Blanc-Mathieu, Romain and Endo, Hisashi and Ohkubo, Koichi and Kanehisa, Minoru and Goto, Susumu and Ogata, Hiroyuki, Bioinformatics, 36(7):2251--2252, 2020 (Pubmed)
Sensitive protein alignments at tree-of-life scale using DIAMOND Buchfink, Benjamin and Reuter, Klaus and Drost, Hajk-Georg, Nature methods, 18(4):366--368, 2021 (Pubmed)
KEGG as a reference resource for gene and protein annotation Kanehisa, Minoru and Sato, Yoko and Kawashima, Masayuki and Furumichi, Miho and Tanabe, Mao, Nucleic acids research, 44(D1):D457--D462, 2015 (Pubmed)
jvenn: an interactive Venn diagram viewer Bardou, Philippe and Mariette, Jérôme and Escudié, Fédéric and Djemiel, Christophe and Klopp, Christophe, BMC bioinformatics, 15(1):293, 2014 (Pubmed)
ETE 3: reconstruction, analysis, and visualization of phylogenomic data Huerta-Cepas, Jaime and Serra, François and Bork, Peer, Molecular biology and evolution, 33(6):1635--1638, 2016 (Pubmed)
The Pfam protein families database: towards a more sustainable future Finn, Robert D and Coggill, Penelope and Eberhardt, Ruth Y and Eddy, Sean R and Mistry, Jaina and Mitchell, Alex L and Potter, Simon C and Punta, Marco and Qureshi, Matloob and Sangrador-Vegas, Amaia and others, Nucleic acids research, 44(D1):D279--D285, 2015 (Pubmed)
Expanded microbial genome coverage and improved protein family annotation in the COG database Galperin, Michael Y and Makarova, Kira S and Wolf, Yuri I and Koonin, Eugene V, Nucleic acids research, 43(D1):D261--D269, 2014 (Pubmed)
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy Emms, David M and Kelly, Steven, Genome biology, 16(1):157, 2015 (Pubmed)
Circos: An information aesthetic for comparative genomics Krzywinski, Martin and Schein, Jacqueline and Birol, Inanç and Connors, Joseph and Gascoyne, Randy and Horsman, Doug and Jones, Steven J and Marra, Marco A, Genome Research, 19(9):1639, 2009 (Pubmed)
RefSeq: an update on prokaryotic genome annotation and curation Haft, Daniel H and DiCuccio, Michael and Badretdin, Azat and Brover, Vyacheslav and Chetvernin, Vyacheslav and O’Neill, Kathleen and Li, Wenjun and Chitsaz, Farideh and Derbyshire, Myra K and Gonzales, Noreen R and others, Nucleic acids research, 46(D1):D851--D860, 2017 (Pubmed)
MAFFT multiple sequence alignment software version 7: improvements in performance and usability Katoh, Kazutaka and Standley, Daron M, Molecular biology and evolution, 30(4):772--780, 2013 (Pubmed)
FastTree 2--approximately maximum-likelihood trees for large alignments Price, Morgan N and Dehal, Paramvir S and Arkin, Adam P, PloS one, 5(3):e9490, 2010 (Pubmed)
KEGG Mapper for inferring cellular functions from protein sequences Kanehisa, Minoru and Sato, Yoko, Protein Science, -(-):-, 2019 (Pubmed)
Nextflow enables reproducible computational workflows Di Tommaso, Paolo and Chatzou, Maria and Floden, Evan W and Barja, Pablo Prieto and Palumbo, Emilio and Notredame, Cedric, Nature biotechnology, 35(4):316, 2017 (Pubmed)
AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence Feldgarden, Michael and Brover, Vyacheslav and Gonzalez-Escalona, Narjol and Frye, Jonathan G. and Haendiges, Julie and Haft, Daniel H. and Hoffmann, Maria and Pettengill, James B. and Prasad, Arjun B. and Tillman, Glenn E. and Tyson, Gregory H. and Klimke, William, Scientific Reports, 11(1):12728, 2021 (Pubmed)
Scoary2: rapid association of phenotypic multi-omics data with microbial pan-genomes Roder, Thomas and Pimentel, Gr{\'e}gory and Fuchsmann, Pascal and Stern, Mireille Tena and von Ah, Ueli and Verg{\`e}res, Guy and Peischl, Stephan and Brynildsrud, Ola and Bruggmann, R{\'e}my and B{\"a}r, Cornelia, Genome Biology, 25(1):93, 2024 (Pubmed)
PaperBLAST: Text Mining Papers for Information about Homologs Morgan N. Price and Adam P. Arkin, mSystems, 2(4):10.1128/msystems.00039-17, 2017 (Pubmed)