ramithuh / diff-evol-tree-searchLinks
We introduce a differentiable approach to phylogenetic tree construction, optimizing tree and ancestral sequences in its original representation itself, thus requiring no prior training data.
☆20Updated last year
Alternatives and similar repositories for diff-evol-tree-search
Users that are interested in diff-evol-tree-search are comparing it to the libraries listed below
Sorting:
- Fast and accurate protein structure prediction☆54Updated 8 months ago
- A structure-based, alignment-free embedding approach for proteins. Can be used as input to machine learning algorithms.☆41Updated 2 years ago
- ☆30Updated last year
- PDBench is a dataset and software package for evaluating fixed-backbone sequence design algorithms.☆30Updated 2 years ago
- ☆43Updated 11 months ago
- ☆22Updated 4 months ago
- Python package to manage protein structures and their annotations☆44Updated last year
- Machine learning prediction of enzyme optimum pH☆45Updated 4 months ago
- A tool for accurate prediction of a protein's secondary structure from only it's amino acid sequence☆59Updated 5 months ago
- GTalign, high-performance protein structure alignment, superposition and search☆50Updated last month
- ☆22Updated 2 years ago
- ☆11Updated 4 years ago
- ☆32Updated last month
- PLMAlign utilizes per-residue embeddings as input to obtain specific alignments and more refined similarity☆20Updated last week
- ML toolset for creating TED: The Encyclopedia of Domains☆22Updated 3 months ago
- Fast and accurate protein domain segmentation using Invariant Point Attention☆41Updated 3 months ago
- Repository for Protein-Vec, a protein embedding mixture of experts model☆38Updated last year
- Embedding-based annotation transfer (EAT) uses Euclidean distance between vector representations (embeddings) of proteins to transfer ann…☆37Updated 3 weeks ago
- Code associated with the paper 'Cracking the blackbox of deep sequence-based protein-protein interaction prediction'☆25Updated last year
- Local homology search powered by ESM-2 language model, foldseek, hhsuite, and hmmer.☆15Updated 8 months ago
- ☆17Updated 2 years ago
- ☆41Updated last week
- Computational tools for extremely low-cost, massively parallel amplicon-based sequencing of every variant in protein mutant libraries.☆34Updated 3 years ago
- Contact map alignment☆16Updated 7 years ago
- Python framework for doing ancestral sequence reconstruction☆41Updated last year
- Results and data from the pilot round of the Protein Engineering Tournament☆30Updated 5 months ago
- Graph-based community clustering approach to extract protein domains from a predicted aligned error matrix☆35Updated 3 years ago
- DE-STRESS is a model evaluation pipeline that aims to make protein design more reliable and accessible.☆27Updated 6 months ago
- ☆16Updated 3 weeks ago
- ☆25Updated 2 years ago