Online tools

Environmental Microbial Genomics Laboratory

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:

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

The following list features some tools developed at Kostas lab:

Nonpareil: Estimating coverage in metagenomes
Estimate the coverage of a Whole Genome Shotgun metagenome and generate projections of sequencing efforts.
MyTaxa: Identifying taxonomy in metagenomic fragments
Assign the most probable taxonomic affiliation of a metagenomic fragment at species, genus, and phylum levels.
ROCker: Accurately detecting functional genes in metagenomes
Accurately identify and quantify target functional genes in metagenomes using data-driven filtering techniques.
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 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.