nmatzke / 3diphyLinks
Maximum likelihood structural phylogenetics by including Foldseek 3Di characters. Supporting Information for Puente-Lelievre et al. 2023n for
☆21Updated 3 months ago
Alternatives and similar repositories for 3diphy
Users that are interested in 3diphy are comparing it to the libraries listed below
Sorting:
- Python framework for doing ancestral sequence reconstruction☆39Updated last year
- Protein structure alignment and search algorithm☆65Updated last week
- Discovery of conserved gene clusters in multiple genomes☆83Updated 2 months ago
- Clustering the NCBI nr database with mmseq2 (90% length, 90% identity). Inspired by the NCBI's experimental ClusteredNR database.☆23Updated 2 years ago
- Universal and efficient structure-based core gene phylogeny with Foldseek and ProstT5☆71Updated last month
- scripts for predicting natural product activity from biosynthetic gene cluster sequences☆23Updated 2 months ago
- Parse NCBI CD-search results to find and visualise the domain architecture of secondary metabolite synthases☆24Updated 2 years ago
- Predict oxygen, temperature, salinity, and pH preferences of bacteria and archaea from a genome☆56Updated 4 months ago
- Software for predicting translation initiation rates in bacteria☆29Updated last week
- Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments.☆35Updated last month
- Web scraper to retrieve protein data catalogued by the CAZy, UniProt, NCBI, GTDB and PDB websites/databases.☆14Updated 7 months ago
- Calculates pairwise sequence identity, similarity and normalized similarity score of proteins in a multiple sequence alignment.☆17Updated last year
- A quick and easy way to download the genomes/predicted proteins of taxa available in JGI's Genome Portal.☆37Updated 2 months ago
- GCsnap: interactive snapshots for the comparison of protein-coding genomic contexts☆30Updated last year
- A flexible and modular software suite for domain-based gene neighborhood and protein search, extraction, and clustering.☆21Updated 4 months ago
- A highly scalable, user-interactive tool for the large scale analysis of Biosynthetic Gene Clusters data☆83Updated 8 months ago
- ☆8Updated 10 months ago
- ☆26Updated last year
- SMBGC Annotation using Neural Networks Trained on Interpro Signatures☆27Updated 4 months ago
- Virus Protein Structural Analysis Toolkit☆11Updated 11 months ago
- MSA(Multiple Sequence Alignment) visualization python package for sequence analysis☆139Updated 8 months ago
- A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima☆57Updated 4 years ago
- snakemake pipeline for creating trees from sequence sets☆85Updated 2 months ago
- The 3DFI pipeline predicts the 3D structure of proteins and searches for structural homology in the 3D space.☆20Updated last year
- Nanopore UMI-linked consensus sequencing☆16Updated 4 years ago
- ProtSpace is program that helps in visualizing and investigating our protein embedding space.☆28Updated this week
- UniProt Id Mapping through API☆34Updated 10 months ago
- Protein Sequence Annotation with Language Models☆23Updated 2 months ago
- Modeling whole bacterial genome as a sequence of proteins.☆48Updated 2 weeks ago
- Ancestral Sequence Reconstruction in Python☆14Updated 6 years ago