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a-pro

ASTRAL for PaRalogs and Orthologs

admixtools

Tools test whether admixture occurred and more

alphafold

Open source code for AlphaFold.

angsd

Program for analysing NGS data.

bioinf2019

dupgen_finder

A pipeline used to identify different modes of duplicated gene pairs

easyspeciestree

Easily construct the ML species tree with single-copy gene shared by different species.

genome-annotation-pipeline

Genome annotation

genomics-analysis-pipeline

Some useful bioinformatics pipelines for genomics analysis

hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

huperziagenome

jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics

merqury

k-mer based assembly evaluation

pepper3dgenome

phylostratr

An R framework for phylostratigraphy

pseudofinder

Detection of pseudogene candidates in bacterial and archaeal genomes.

pseudogenepipeline

psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

psonic

The repository serves as a public and official hosting of the pSONIC program (Conover et al., 2021).

relative-rate-test

Tajima Relative Rate Test Of Molecular Clock

subphaser

Phase and visualize subgenomes of an allopolyploid or hybrid based on the repetitive kmers.

syn-mrl

Synteny matrix representation with maximum likelihood pipeline

synnet-pipeline

Workflow for Building Microsynteny Networks

test

my test

to-gcn

Pipeline of time-ordered gene coexpression network (TO-GCN) construction from three-dimensional (gene expression, condition, and time) data

trinityrnaseq

Trinity RNA-Seq de novo transcriptome assembly

tutorials

Tutorials on phylogenetic and phylogenomic inference

wgd

Python package and CLI for whole-genome duplication related analyses

wgdi

Finely identify the whole genome duplication events and generate the genomic homology tables.