Evaluation script for named entity recognition (NER) systems based on entity-level F1 score.

Full named-entity (i.e., not tag/token) evaluation metrics based on SemEval’13

Dataframes powered by a multithreaded, vectorized query engine, written in Rust

CLI interface for running SQL queries with Polars as backend

A Python library for phylogenetic scripting, simulation, data processing and manipulation.

Simple phylogenetic tree visualization python package for phylogenetic analysis

Processed data and R notebooks to reproduce analyses from our publication "Acquisition of a complex root microbiome reshapes the transcriptional landscape of rice plants"

TransDecoder source

Convert GTDB taxonomy to NCBI taxdump format

Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy

Interactively explore metagenomes and more from a web browser.

typeahead.js is a fast and fully-featured autocomplete library

RAxML Next Generation: faster, easier-to-use and more flexible

A stupidly small and simple jQuery table sorter plugin

A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0

Built-in Movie Graph Example

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

PGPg Finder is a command-line tool that offers different workflows for genome and metagenome annotation of Plant-Growth Promotion Genes. It's designed to be flexible and easy to use pipeline, with …

ASTRAL for PaRalogs and Orthologs

A set of tools for processing amplicon data

Normalization of RNA-seq gene expression

Versatile open-source tool for microbiome analysis

🌈 Interactive analysis of metagenomics data

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

A genome completeness evaluation tool based on miniprot