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

Taxonomy classification of viral sequences / contigs

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

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

Shiny app that matches scientific names to the EPICC taxonomy

Former version of METAPIPE

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

taxalogue - a toolkit to create comprehensive CO1 reference databases

#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…

Fetch taxonomic information from Entrez using a list of TaxIDs and visualize user-selected taxonomic ranks with SankeyMATIC.

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.

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

Taxonomy assignment with task queue

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

Microbiome analysis pipeline with reference tutorial. This code was written in October 2024 to process rRNA marker gene data (16S and ITS) from rhizosphere soil samples.