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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:
- 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