Alternatives and similar repositories for 3diphy:

Users that are interested in 3diphy are comparing it to the libraries listed below

• Arcadia-Science / 2023-nr-clustering
  Clustering the NCBI nr database with mmseq2 (90% length, 90% identity). Inspired by the NCBI's experimental ClusteredNR database.
  ☆23Updated last year
• steineggerlab / unicore
  Universal and efficient core gene phylogeny with Foldseek and ProstT5
  ☆48Updated last week
• harmslab / topiary
  Python framework for doing ancestral sequence reconstruction
  ☆37Updated 7 months ago
• BolognaBiocomp / deepsig
  DeepSig - Predictor of signal peptides in proteins based on deep learning
  ☆26Updated last year
• psipred / merizo_search
  Fast protein domain structure embedding+search tool
  ☆12Updated last month
• corydunnlab / SequenceBouncer
  A Python3 script for removal of outlier sequences from a multiple sequence alignment (FASTA format).
  ☆9Updated 3 weeks ago
• cbcrg / msa-af2-nf
  Nextflow pipeline for the computation of structure-based MSAs with AlphaFold2 models
  ☆12Updated 2 years ago
• Protein-Sequence-Annotation / PSALM
  Protein Sequence Annotation with Language Models
  ☆19Updated 3 months ago
• althonos / pyfamsa
  Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments.
  ☆30Updated this week
• Zsailer / pyasr
  Ancestral Sequence Reconstruction in Python
  ☆13Updated 5 years ago
• PombertLab / 3DFI
  The 3DFI pipeline predicts the 3D structure of proteins and searches for structural homology in the 3D space.
  ☆19Updated 11 months ago
• andyposbe / ColabFold-Pipeline-Toolkit
  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
• Gaius-Augustus / learnMSA
  Learning and Aligning Large Protein Families with support of protein language models.
  ☆20Updated last week
• soedinglab / spacedust
  Discovery of conserved gene clusters in multiple genomes
  ☆59Updated last week
• JoanaMPereira / GCsnap
  GCsnap: interactive snapshots for the comparison of protein-coding genomic contexts
  ☆26Updated 10 months ago
• Finn-Lab / SanntiS
  SMBGC Annotation using Neural Networks Trained on Interpro Signatures
  ☆23Updated this week
• ThomasCMcLean / LazyAF
  Code for LazyAF pipeline
  ☆21Updated last year
• althonos / pymuscle5
  Cython bindings and Python interface to MUSCLE v5, a highly efficient and accurate multiple sequence alignment software.
  ☆20Updated 9 months ago
• jbloomlab / SARS2-mut-fitness
  Observed substitution counts of SARS-CoV-2 compared to those expected under the mutation rates
  ☆19Updated 3 months ago
• Benjamin-Lee / CodonAdaptationIndex
  Python Implementation of Codon Adaption Index
  ☆36Updated 2 years ago
• althonos / pytrimal
  Cython bindings and Python interface to trimAl, a tool for automated alignment trimming. Now with SIMD!
  ☆22Updated 5 months ago
• ablab / nerpa
  ☆15Updated 11 months ago
• amaurypm / pseqsid
  Calculates pairwise sequence identity, similarity and normalized similarity score of proteins in a multiple sequence alignment.
  ☆14Updated last year
• TravisWheelerLab / nail
  Nail is an Alignment Inference tooL
  ☆44Updated 3 weeks ago
• kaistsystemsbiology / DeepProZyme
  DeepECtransformer
  ☆23Updated last year
• althonos / mini3di
  A NumPy port of the foldseek code for encoding protein structures to 3di.
  ☆38Updated 4 months ago
• salzberg-lab / Balrog
  Bacterial Annotation by Learned Representation of Genes
  ☆54Updated 4 years ago
• barricklab / ostir
  Software for predicting translation initiation rates in bacteria
  ☆21Updated 2 months ago
• EngqvistLab / Tome
  A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima
  ☆55Updated 4 years ago
• JLSteenwyk / orthohmm
  Improved Inference of Ortholog Groups using Hidden Markov Models
  ☆32Updated last month