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.

SolexaQA++

Cox MP, Peterson DA, and Biggs PJ (2010). SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics 11:485.

Scythe

GitHub: vsbuffalo/scythe, by Vince Buffalo.

FastQC

FastQC site, by Simon Andrews.

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.

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.