Sparse InversE Covariance estimation for Ecological Association and Statistical Inference

NCBI Prokaryotic Genome Annotation Pipeline

HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.

A versatile framework for single-cell transcriptomic data analysis in plants.

Official code repository for GATK versions 4 and up

PASA software

Neural network classification of TE

High-precision TE Annotator

Minor edits to allow MITE_Hunter (Han & Wessler 2010) to use modern blast+

A parallel wrapper for LTR_FINDER

Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/

标注自己的数据集，训练、评估、测试、部署自己的人工智能算法

Version 5 of the CAFE phylogenetics software

Program for finding horizontal gene transfer using BLAST result

Python package and CLI for whole-genome duplication related analyses. **This package is deprecated in favor of** https://github.com/heche-psb/wgd.

Extensive de-novo TE Annotator

ParaFly - parallel cmd processing utility

TransDecoder source

GenomeTools genome analysis system.

Copy number variant detection from targeted DNA sequencing

Genome annotation pipeline

Accurate Species TRee ALgorithm

Automatically exported from code.google.com/p/prottest3

Scripts to download genomes from the NCBI FTP servers

zgtools: A pipeline that allows for the convenient acquisition of T2T (Telomere-to-Telomere) genomes.