Application and Python module for average nucleotide identity analyses of microbes.

Assign taxonomy with blast, can be used for qiime

CyanoSeq: A curated cyanobacterial 16S rRNA database for next-generation sequencing

An HMM and Phylogenetic Placement based Ultra-Fast Taxonomy Assignment Tool for 16S sequencing

nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.

Taxonomic classification of metagenomic contigs

Shiny app that matches scientific names to the EPICC taxonomy

Tool to automatically extract keyphrases from text spanning across vast domains, and generate an ontology.

#Scripts to create Kraken2 database of PAFTOL V2.0 Angio353 genes. An excellent database for taxonomic identification of plants. #https://treeoflife.kew.org/ #https://github.com/DerrickWood/kraken2/wiki #Prior to using this script, download and install kraken2 and make sure it is working and in your PATH. #Make sure the location of the python sc…

Taxonomy assignment with task queue

metaTag: functional and taxonomical annotation of metagenomes through phylogenetic tree placement

Former version of METAPIPE

Sequence Matching fOr REpiratory Diseases, SMORE'D, is a command-line sequence classification tool tailored to meet the needs of the Undiagnosed Respiratory Disease Outbreak (URDO) branch at CDC. SMORE'D is a k-mer based classification tool capable of rapidly classifying read sequences generated by multi-pathogen detection platforms.

taxalogue - a toolkit to create comprehensive CO1 reference databases

Checking the presence of a species in a metagenomics sample with known taxonomic composition

To identify taxa of given sequences via BOLD system (http://www.boldsystems.org/index.php)

Correlates target taxonomy(i.e consensus lineages) with a reference taxonomy such as Greengenes, SILVA, etc.

In this tutorial it is provided an overview of the anvi’o workflow for the analysis of assembly-based shotgun metagenomic data.

Next Generation Phylogenetic Microbiome Analysis Framework