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

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

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

Taxonomic classification of metagenomic contigs

An open-source framework designed to extend and maintain the ESCO taxonomy

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

taxalogue - a toolkit to create comprehensive CO1 reference databases

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

Legacy repo for hosting versions of the IHerbSpec Protocol

Former version of METAPIPE

A local-first tool for managing literature reviews, tagging papers, and exploring design spaces.

#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 scripts used below are also in your PATH #Download PAFTOL V2.0 Angio353 genes from Kew #After building the DB, the scripts kraken2paired.py and top_taxa.py can be used to identify taxonomy of unknown samples. #e.g. #kraken2paired.py "reads/*.fastq" kraken_results/ 0 24 kraken2_paftol2/ #top_taxa.py "kraken_results/*" kraken.out

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.

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

Taxonomy assignment with task queue

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

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

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

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.

No description provided.

A Statamic (4.x and 5.x) addon

Find the best taxonomic assignement for the given genomic sequence based on maximum F-measure.

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

Python module that provide an alternative view of the outputs produced by the software pyani