xdli009

DeepHost

This is the repository for DeepHost, a phage host prediction tool.

PPNet

Identifying functional association networks by phylogenetic profiling of prokaryotic genomes

CRISPRidentify

nonpareil

Estimate metagenomic coverage and sequence diversity

ViWrap

A wrapper to identify, bin, classify, and predict host-viral relationship for viruses

vRhyme

Binning Virus Genomes from Metagenomes

codonw-slim

A slimmed down fork of CodonW with python bindings

ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

abritamr

A pipeline for running AMRfinderPlus and collating results into functional classes

gpt_academic

为GPT/GLM等LLM大语言模型提供实用化交互接口，特别优化论文阅读/润色/写作体验，模块化设计，支持自定义快捷按钮&函数插件，支持Python和C++等项目剖析&自译解功能，PDF/LaTex论文翻译&总结功能，支持并行问询多种LLM模型，支持chatglm3等本地模型。接入通义千问, deepseekcoder, 讯飞星火, 文心一言, llama2, rwkv, claude2, moss等。

Integron_Finder

Bioinformatics tool to find integrons in bacterial genomes

emg-viral-pipeline

VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies

svim-asm

Structural Variant Identification Method using Genome Assemblies

dipcall

Reference-based variant calling pipeline for a pair of phased haplotype assemblies

VIBRANT

Virus Identification By iteRative ANnoTation

vpf-tools

Virus Protein Family tools

ecoli_serotyping

In silico prediction of E. coli serotype

CHERRY_crispr_DATABASE

Database version of CHERRY CRISPR

spacepharer

SpacePHARER CRISPR Spacer Phage-Host pAiRs findER

CHERRY

Host prediction for phages

PhaGCN

GCN classifier for phage taxanomy classification

PhageTailFinder

A software for phage tail module recognition based on hidden markov model

deeplasmid

alphafold

Open source code for AlphaFold.

MADroot

Efficient implementation of the MAD method for inferring the location of the root in a large phylogeny.

bnkit

Bayesian network toolkit, with applications for phylogenetic analysis

Unicycler

hybrid assembly pipeline for bacterial genomes

BESST

BESST - scaffolder for genomic assemblies

Circle_finder

Micro DNA identification

PropagAtE

Prophage Activity Estimator