Find clustered hits from a BLAST search

A user-friendly workflow for phylogenomics

🔥🕷️ Crawl4AI: Open-source LLM Friendly Web Crawler & Scrapper

Automatically Stopping MCMC/MC3

Accurate sample inference from amplicon data with single nucleotide resolution

Scripts for MAUI-seq metabarcoding analysis

Visualing species tree from ASTRAL with gene tree discordance

A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets

Cluster long amplicons using dada2 denoising on variable regions

A tool to filter BUSCO output into single-copy gene files for phylogenomics

Cython bindings and Python interface to HMMER3.

general purpose library for evaluating the likelihood of sequence evolution on trees

Fungal species-level taxonomic profiling method for metagenomes and metatranscriptomes using multiple short hypervariable rRNA regions

Plotting scripts for long read sequencing data

Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz).

Evaluation and polishing workflows for T2T genome assemblies

BSc Project at Leiden University for generating and updating a fungal phylogenetic tree based on MDDB

Implementation of the TreeShrink problem

High-quality Nanopore-only genome polisher

quality filtering tool for long reads

A Comprehensive Toolkit for High-Quality PDF Content Extraction

rattler-build is a universal package builder for Windows, macOS and Linux

Implementation of Alphafold 3 in Pytorch

Extracting Tables from Document Images using a Multi-stage Pipeline for Table Detection and Table Structure Recognition:

Determine presence of telomeres and visualise genome assembly scaffolds.