External Software

Enveomics Collection

Rodriguez-R LM, and Konstantinidis KT (2016). The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 4:e1900v1.

NCBI BLAST+

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, and Madden TL (2009). BLAST+: architecture and applications. BMC Bioinformatics 10:421.

HMMer 3

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.

FaQCs

Chienchi L and Chain PSG (2014). Rapid evaluation and Quality Control of Next Generation Sequencing Data with FaQCs. BMC Bioinformatics 15:366.

Seqtk

GitHub: lh3/seqtk by Heng Li et al.

fastp

Chen S, Zhou Y, Chen Y, Gu J (2018). fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34(17):i884–i890

Falco

de Sena BG and Smith AD (2021). Falco: high-speed FastQC emulation for quality control of sequencing data. F1000Research 8:1874

multitrim

GitHub: KGerhardt/multitrim, by Kenji Gerhardt et al.

IDBA-UD

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.

Prodigal

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.

Barrnap

GitHub: tseemann/barrnap, by Torsten Seemann.

Bedtools

Bedtools site, by the Quinlan Laboratory.

RDP Classifier

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.

MyTaxa

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.

Krona

Ondov BD, Bergman NH, and Phillippy AM (2011). Interactive metagenomic visualization in a Web browser. BMC Bioinformatics 12:385.

MCL

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.

Ape

Paradis E, Claude J, and Strimmer K (2004). APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics 20(2):289-290.

Vegan

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.

Diamond

Buchfink B, XieC, and Huson DH (2015). Fast and Sensitive Protein Alignment using DIAMOND. Nature Methods 12:59–60.

FastANI

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.

FastAAI

GitHub: cruizperez/FastAAI, by Carlos Ruiz-Perez et al.

tRNAscan-SE

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.