biogeeker

ASTRAL

Accurate Species TRee ALgorithm

codon-bias

Python package of codon usage bias analysis tools

TomatoSuperPanGenome

Here, we sequence and de novo assemble chromosome-scale genomes of nine wild species and two cultivated accessions of tomato and constructed a pan-genome, revealing phylogenetic relationships and structural variation among Lycopersicon

Uni-Fold

An open-source platform for developing protein models beyond AlphaFold.

provis

Official code repository of "BERTology Meets Biology: Interpreting Attention in Protein Language Models."

RaptorX-Single

DNNGP

DNNGP: Deep neural network for genomic prediction

deepgoplus

DeepGO with GOPlus axioms

PeSTo

localcolabfold

ColabFold on your local PC

deeplearning-biology

A list of deep learning implementations in biology

af2complex

Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.

EigenFold

EigenFold: Generative Protein Structure Prediction with Diffusion Models

EquiBind

EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein

rgn2

ParallelFold

Modified version of Alphafold to divide CPU part (MSA and template searching) and GPU part. This can accelerate Alphafold when predicting multiple structures

minGPT

A minimal PyTorch re-implementation of the OpenAI GPT (Generative Pretrained Transformer) training

awesome-chatgpt-prompts

This repo includes ChatGPT prompt curation to use ChatGPT better.

hsm

Code associated with "Biophysical prediction of protein-peptide interactions and signaling networks using machine learning."

AutoX

AutoX is an efficient automl tool, which is mainly aimed at data mining tasks with tabular data.

Agora

Algorithm For Gene Order Reconstruction in Ancestors

gggenomes

A grammar of graphics for comparative genomics

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

OmegaFold

OmegaFold Release Code

tape

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

qvina

Accurately speed up AutoDock Vina

EternaFold

Improving RNA structure prediction through multitask learning on diverse crowdsourced data.

wgdi-example

ProteinLM

Protein Language Model

ShinySyn

A shiny application to visualize MCscan result