External Software
Rodriguez-R LM, and Konstantinidis KT (2016). The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 4:e1900v1.
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, and Madden TL (2009). BLAST+: architecture and applications. BMC Bioinformatics 10:421.
Mistry J, Finn RD, Eddy SR, Bateman A, and Punta M (2013). Challenges in Homology Search: HMMER3 and Convergent Evolution of Coiled-Coil Regions. Nucleic Acids Res 41:e121.
Chienchi L and Chain PSG (2014). Rapid evaluation and Quality Control of Next Generation Sequencing Data with FaQCs. BMC Bioinformatics 15:366.
Chen S, Zhou Y, Chen Y, Gu J (2018). fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34(17):i884–i890
de Sena BG and Smith AD (2021). Falco: high-speed FastQC emulation for quality control of sequencing data. F1000Research 8:1874
Peng Y. Leung HC, Yiu SM, and Chin FY (2012). IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics, 28:1420-1428.
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ (2010). Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics, 11(1):119.
Wang Q, Garrity GM, Tiedje JM, and Cole JR (2007). Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy. Appl Environ Microbiol 73(16):5261-7.
Luo C, Rodriguez-R LM, and Konstantinidis KT (2014). MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res, 42(8):e73.
Ondov BD, Bergman NH, and Phillippy AM (2011). Interactive metagenomic visualization in a Web browser. BMC Bioinformatics 12:385.
Enright AJ, Van Dongen S, and Ouzounis CA (2002). An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30(7):1575-1584.
Paradis E, Claude J, and Strimmer K (2004). APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics 20(2):289-290.
Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, Minchin PR, O'Hara RB, Simpson GL, Solymos P, Stevens MHM, Szoecs E, and Wagner H (2017). Vegan: Community Ecology Package. R package.
Buchfink B, XieC, and Huson DH (2015). Fast and Sensitive Protein Alignment using DIAMOND. Nature Methods 12:59–60.
Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, and Aluru S (2018). High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nature Comm 9:5114.
Chan PP, Lin BY, Mak AJ, and Lowe TM (2021). tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic Acids Res 49:9077–9096.
Last modified 4mo ago