Using Deep Learning to predict gene annotations

Tool for fully-automated inference of species trees from raw genome assemblies

gghic makes visualization of Hi-C/-like data easily in R

Strand and WGD aware syntenic gene identification

A toolkit to easily access, convert and compare the de novo gene annotation format (dngf)

genome annotation (RNAseq and TE) pipeline (draft)

Multi-level visualization of genomic statistical variables on rectangular chromosomes

Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome

TwinC: Twin CNN model for 3D genome folding

Pairwise whole genome aligner

C-Phasing/CPhasing: Phasing and scaffolding polyploid genomes based on Pore-C, HiFi-C/CiFi or Hi-C.

A pipeline for genomic variant detection with genome assemblies at population scale

The scripts that were used in the final Bhyb26 publication. Includes not only scripts that produced the figures, but also the scripts that produced the data used in the figures, i.e. analysis pipel…

info and docs for the Wright Lab

tool for dating gene age by micro- and macro-synteny with high speed and accuracy

Phylogenetic model exploration with deep learning

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

Finding Recurrent Substitutions in Multiple Sequence Alignments

Collection of scripts to analyse convergent traits. work in progress, right now it still only has one tool

This is the standalone version of the EviAnn pipeline

plot genome alignment synteny

SyntenyFinder contains a collection of scripts for performing and visualizing macrosynteny analyses. It supports annotated chromosome-level genome assemblies from NCBI and offers customization opti…