CrawlingSponge

3DVizSNP

AdmixTools

Tools test whether admixture occurred and more

autocoalhmm

Automated pipeline for running CoalHMM

NGS-analysis

二代测序数据分析

Ohnologs-v2.0

The code repository for OHNOLOGS v2.0 sever and multi-genome synteny comparison.

FastEPRR

My published program for estimating the population recombination rate.

vcflib

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

odo_introgression

Pipeline code for Deep ancestral introgression shapes evolutionary history of dragonflies and damselflies

HyDe

Hybridization detection using phylogenetic invariants

DESCHRAMBLER

miniprot

Align proteins to genomes with splicing and frameshift

GALBA

GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the scenario where high quality proteins from one or several closely related species are available.

evals

Evals is a framework for evaluating LLMs and LLM systems, and an open-source registry of benchmarks.

RASP

Reconstruct Ancestral State in Phylogenies

dfoil

DFOIL: Introgression Testing for Five Taxa

drosophila_phylogeny

Pipeline overview and code (including BLT-DCT program) for widespread introgression across a phylogeny of 155 Drosophila genomes

biopython

Official git repository for Biopython (originally converted from CVS)

TaoNet

Simulate gene family syntenic networks.

Syn-MRL

Synteny matrix representation with maximum likelihood pipeline

SynNet-Pipeline

Workflow for Building Microsynteny Networks

muscle

Multiple sequence alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.

tutorials

Tutorials on phylogenetic and phylogenomic inference

bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

G-PhoCS

G-PhoCS is a software package for inferring ancestral population sizes, population divergence times, and migration rates from individual genome sequences.

RAD_Tools

A collection of usefull tools for RAD or GBS data analysis

novowrap

Assembly chloroplast genome and validate conformation

genomepy

genes and genomes at your fingertips

iTOL

A Python API and a command-line tool for the Tree of Life

vgp-assembly

VGP repository for the genome assembly working group

Buxus-Tetracentron-Genomes

Repository of scripts and command-line agruments used in the manuscript "Buxus and Tetracentron genomes help resolve eudicot genome history"