Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.

Topology weighting by iterative sampling of sub-trees

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

Long-reads Gap-free Chromosome-scale Assembler

Best practices and workflow for genome annotation

Algorithm For Gene Order Reconstruction in Ancestors

A fast and efficient tool for converting chromatin interaction data between genome assemblies

a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies

A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes

convert various features into a GFF-like file for use in genome browsers

Tools to analyze Dip-C (or other 3C/Hi-C) data

A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget and RcisTarget.

An accessible and flexible tool for fitting demographic models with dadi using custom or published models (available here), conducting goodness of fit tests, and plotting.

A tool to extract and visualize the results of CAFE (Computational Analysis of gene Family Evolution)

An efficient way to convert gff3 annotation files into EMBL format ready to submit.

Protein hint generation pipeline for gene finding in eukaryotic genomes

A modular, containerized pipeline for ATAC-seq data processing

Portable solution to generate genome alignment chains using lastz

Structural variant caller

create, manage, and upload track hubs for use in the UCSC genome browser

My bioinfo toolbox

TSEBRA: Transcript Selector for BRAKER

TADtool is an interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data.

Plant genome assembly and annotation pipeline using snakemake

scripts for the project of seven thaliana genomes assembly