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Citations

If you use the online tools in this website, please cite the article below and/or the article describing the specific algorithm/tool used (see corresponding webpages), as appropriate:

Reference

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

Our tools

The following list features some tools developed at Kostas lab:

ANI: Average Nucleotide Identity calculator

Estimate the distribution of nucleotide identity between fragments of two genomic sequences.

AAI: Average Amino acid Identity calculator

Estimate the distribution of amino acid identity between proteins from two genomic sequences.

ANI/AAI-Matrix: All-vs-all ANI/AAI matrix calculator

Estimate the average nucleotide or amino acid identities between each pair in a collection of genomes (or proteomes).

The Microbial Genomes Atlas - MiGA

Process, evaluate, and taxonomically classify genomes using genome-wide comparisons.

The enveomics collection: A toolbox for microbial genomics and metagenomics

Collection of scripts developed at Kostas lab for microbial genomics and metagenomics, now including a Graphic User Interface.

Nonpareil: Estimating coverage in metagenomes

Estimate the coverage of a Whole Genome Shotgun metagenome and generate projections of sequencing efforts.

ROCker: Accurately detecting functional genes in metagenomes

Accurately identify and quantify target functional genes in metagenomes using data-driven filtering techniques.

MyTaxa: Identifying taxonomy in metagenomic fragments

Assign the most probable taxonomic affiliation of a metagenomic fragment at species, genus, and phylum levels.

imGLAD: in-silico metagenomes for Genome Low-Abundance Detection

Accurate detection and quantification of target organisms in metagenomes