Phyla: Towards a Foundation Model for Phylogenetic Inference
☆28Nov 20, 2025Updated 4 months ago
Alternatives and similar repositories for Phyla
Users that are interested in Phyla are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- PLM-interact: extending protein language models to predict protein-protein interactions.☆65Aug 29, 2025Updated 7 months ago
- ☆12Nov 16, 2023Updated 2 years ago
- ☆13Jul 24, 2025Updated 8 months ago
- FAPLM: A Drop-in Efficient Pytorch Implementation of Protein Language Models☆167Mar 28, 2026Updated 3 weeks ago
- Code for humanization of antibody and nanobody☆78Aug 28, 2025Updated 7 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- ☆111Mar 25, 2026Updated 3 weeks ago
- ☆10Dec 20, 2022Updated 3 years ago
- Residue Level Alignment☆22Nov 21, 2024Updated last year
- R and Python scripts used to simulate gene trees under coalescent model and detect gene flow using triple frequency☆15Dec 15, 2022Updated 3 years ago
- This is the GitHub repository accompanying Krishnan, Anahtar, Valeri, et al., 2025☆37Jun 8, 2025Updated 10 months ago
- [ICML 25] We train and evaluate SAEs to identify interpretable features in pLMs and show their potential for scientific discovery.☆126Jan 16, 2026Updated 3 months ago
- Implementation code for the paper "Aggregating Residue-Level Protein Language Model Embeddings with Optimal Transport"☆22May 3, 2025Updated 11 months ago
- ☆12Sep 14, 2025Updated 7 months ago
- Iterative Gene clUster Analysis, a high-throughput method for gene cluster family identification.☆17Feb 26, 2026Updated last month
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- A massively parallel tool for model selection and tree inference on thousands of genes☆51Mar 4, 2024Updated 2 years ago
- blastn2dotplots: multiple dot-plot visualizer☆24Sep 15, 2025Updated 7 months ago
- ☆10Sep 19, 2020Updated 5 years ago
- ☆11Aug 26, 2024Updated last year
- phyloGAN is a Generative Adversarial Network (GAN) that infers phylognetic relationships.☆11Jul 8, 2024Updated last year
- Size-Wise Analysis of Transfer Learning of pLM Embeddings☆12Jun 10, 2025Updated 10 months ago
- Repository for "Nearest neighbor search on embeddings rapidly identifies distant protein relations"☆13Apr 2, 2023Updated 3 years ago
- Alignment-Based Sequence extraction☆15Feb 14, 2022Updated 4 years ago
- ☆18Dec 8, 2021Updated 4 years ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- Tools for F1 hybrid PSMC (hPSMC) divergence time inference from whole genomes☆15May 29, 2024Updated last year
- Detecting transposable element invasions without repeat library. Detects also horizontal transfer events and endogenized viruses. All you…☆17Nov 25, 2024Updated last year
- CLIP-based model for aligning epitopes to immune receptors☆12Apr 30, 2025Updated 11 months ago
- Computational Analysis of Gene Expression Evolution☆45Aug 19, 2025Updated 7 months ago
- mBER - Manifold Binder Engineering and Refinement. mBER enables antibody binder design by leveraging structure templates and sequence con…☆120Jan 9, 2026Updated 3 months ago
- baltic - adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. This fork will no longe…☆12Dec 18, 2019Updated 6 years ago
- Evolutionary Algorithm with Diffusion Models for Protein Design☆30Jan 7, 2026Updated 3 months ago
- A collection of easy-to-use custom ggplot2-based functions for data exploration and analysis. Each function handles data preprocessing an…☆24Dec 23, 2025Updated 3 months ago
- ☆39Jan 27, 2026Updated 2 months ago
- Wordpress hosting with auto-scaling - Free Trial • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- Locus and lineage tests for bacterial GWAS☆28Oct 5, 2017Updated 8 years ago
- Wrapper script to concatenate, align, and construct phylogenetic trees of BUSCOs☆20Sep 18, 2019Updated 6 years ago
- Semi-Automatic Taxonomy Improvement and Validation Algorithm☆21Jan 8, 2024Updated 2 years ago
- Official open-source of Antibody Design Using a Score-based Diffusion Model Guided by Evolutionary, Physical, and Geometric Constraints☆51Jun 30, 2025Updated 9 months ago
- Codebase of paper "Structure Language Models for Protein Conformation Generation" (ICLR'25)☆76Feb 24, 2025Updated last year
- ☆13Apr 9, 2026Updated last week
- Trim, Align to genome, Deduplicate, Realign WGS sequencing samples☆17Feb 23, 2026Updated last month