harmslab / topiary
Python framework for doing ancestral sequence reconstruction
☆38Updated 9 months ago
Alternatives and similar repositories for topiary:
Users that are interested in topiary are comparing it to the libraries listed below
- Transmembrane proteins predicted through Language Model embeddings☆35Updated 3 months ago
- A domain parser for Alphafold models☆35Updated last year
- ☆38Updated 7 months ago
- Fast protein domain structure embedding+search tool☆18Updated last month
- Detection of remote homology by comparison of protein language model representations☆51Updated 4 months ago
- snakemake pipeline for creating trees from sequence sets☆76Updated last week
- ☆20Updated 2 weeks ago
- Evolutionary conservation estimation of residues or nucleotides☆41Updated 3 years ago
- Fast indexing and search of discontinuous motifs in protein structures☆22Updated 2 months ago
- Protein discovery tool for mining in the Alphafold database based on the position of few amino acids.☆22Updated last week
- A tool for accurate prediction of a protein's secondary structure from only it's amino acid sequence☆54Updated last month
- PyMissense creates the pathogenicity plot and modified pdb as shown in the AlphaMissense paper for custom proteins.☆23Updated last year
- GTalign, HPC protein structure alignment, superposition and search (alpha release)☆42Updated 3 months ago
- ☆27Updated 11 months ago
- ☆30Updated last year
- PLMAlign utilizes per-residue embeddings as input to obtain specific alignments and more refined similarity☆20Updated 4 months ago
- A NumPy port of the foldseek code for encoding protein structures to 3di.☆51Updated 2 months ago
- Rendering protein mutation movies from predicted 3D structures☆20Updated last year
- ☆22Updated last year
- Maximum likelihood structural phylogenetics by including Foldseek 3Di characters. Supporting Information for Puente-Lelievre et al. 2023n…☆20Updated 10 months ago
- Python code to color a PDB structure based on parameters from a multiple sequence alignment☆32Updated last year
- Feature map and function annotation of Proteins☆33Updated 10 months ago
- A software-suite to perform multiple protein structure alignment and structure feature extraction.☆29Updated last year
- Observed substitution counts of SARS-CoV-2 compared to those expected under the mutation rates☆20Updated 5 months ago
- MSA(Multiple Sequence Alignment) visualization python package for sequence analysis☆124Updated 5 months ago
- Code for LazyAF pipeline☆20Updated last year
- The aim of this repository is to provide simple tools to help those working with ColabFold BATCH both for pre and post-processing steps.☆16Updated last year
- Conservation analysis of homologous proteins with Python☆10Updated 3 years ago
- Rapid protein-protein interaction network creation from multiple sequence alignments with Deep Learning☆83Updated last year
- ProtNote is a multimodal deep learning model that leverages free-form text to enable both supervised and zero-shot protein function predi…☆36Updated this week