Making Protein folding accessible to all!
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Dec 18, 2024 - Jupyter Notebook
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multiple-sequence-alignment
Here are 87 public repositories matching this topic...
Generation of protein sequences and evolutionary alignments via discrete diffusion models
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Oct 7, 2024 - Python
A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0
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Dec 20, 2024 - C++
Algorithm for ultra-scale multiple sequence alignments (3M protein sequences in 5 minutes and 24 GB of RAM)
bioinformatics proteomics longest-common-subsequence pfam multiple-sequence-alignment sequence-similarity guide-tree
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Sep 18, 2024 - C++
abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
simd long-reads multiple-sequence-alignment partial-order-alignment consensus-sequences banded-dp consensus-sequence alignment-graph gfa-format
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Dec 10, 2024 - C
MSA(Multiple Sequence Alignment) visualization python package for sequence analysis
visualization python bioinformatics genomics matplotlib sequence-alignment msa sequence-analysis multiple-sequence-alignment
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Dec 1, 2024 - Python
A Julia package to analyze protein sequences, structures, and evolutionary information
bioinformatics biology proteins pdb protein-structure julia-language conservation mutual-information structural-bioinformatics protein-evolution pfam sifts multiple-sequence-alignment coevolution protein-sequence-analysis
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Oct 23, 2024 - Julia
Implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTorch (NeurIPS 2021)
machine-learning bioinformatics pytorch biological-sequences hierarchical-clustering multiple-sequence-alignment neurips-2021
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Oct 14, 2023 - Python
Exploring Evolution-aware & free protein language models as protein function predictors
benchmark pytorch contact-prediction stability multiple-sequence-alignment protein-annotation function-prediction protein-classification alphafold protein-language-model alphafold2 fitness-prediction zero-shot-prediction msa-construction msa-transformer esm1b remote-homology-detection metal-ion-binding
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Sep 28, 2024 - Python
Scalable long read self-correction and assembly polishing with multiple sequence alignment
assembly ngs consensus correction long self msa reads contigs long-reads multiple-sequence-alignment polishing self-correction
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Feb 6, 2024 - C++
Fast and accurate protein structure prediction
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Jul 25, 2023 - Python
🧬 MSABrowser: dynamic and fast visualization of sequence alignments, variations, and annotations
bioinformatics genetics sequence-alignment msa protein-domains multiple-sequence-alignment msa-viewer sequence-alignment-visualization msabrowser
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May 21, 2024 - JavaScript
Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments.
bioinformatics genomics python-library python-bindings sequence-alignment cython-library multiple-sequence-alignment
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Nov 6, 2024 - Cython
Multiple sequence alignment visualizer
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Jan 26, 2023 - JavaScript
TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain
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Jun 17, 2024 - C
Improved RNA Secondary Secondary Structure Prediction using Evolutionary Profile, Mutational Coupling and Two-dimensional Transfer Learning
deep-learning transfer-learning multiple-sequence-alignment rna-secondary-structure canonical-base-pairs pseudoknot-base-pairs lone-pairs direct-coupling-analysis evolutionary-information non-canonical-base-pairs homologous-sequence spot-rna2 base-triples
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Apr 3, 2021 - Perl
Talleres Internacionales de Bioinformática - Centro de Ciencias Genómicas, UNAM, Cuernavaca, México
bioinformatics tutorials linux-shell phylogenetics model-selection blast maximum-likelihood phylogenomics bioinformatics-scripts bash-scripting pangenomics multiple-sequence-alignment reciprocal-blast-hits
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Dec 14, 2024 - Shell
Cython bindings and Python interface to trimAl, a tool for automated alignment trimming. Now with SIMD!
python bioinformatics genomics python-library simd python-interface cython-wrapper multiple-sequence-alignment alignment-trimming
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Aug 28, 2024 - Cython
TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain
tandem-repeats long-reads multiple-sequence-alignment nanopore-sequencing seed-and-chain partial-order-alignment
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Jun 17, 2024 - C
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