Projects in Awesome Lists by soedinglab
A curated list of projects in awesome lists by soedinglab .
https://github.com/soedinglab/mmseqs2
MMseqs2: ultra fast and sensitive search and clustering suite
alignment bioinformatics blast linclust metagenomics mmseqs profile-search sequence-clustering sequence-search taxonomy
Last synced: 05 Oct 2025
https://github.com/soedinglab/MMseqs2
MMseqs2: ultra fast and sensitive search and clustering suite
alignment bioinformatics blast linclust metagenomics mmseqs profile-search sequence-clustering sequence-search taxonomy
Last synced: 05 May 2025
https://github.com/soedinglab/hh-suite
Remote protein homology detection suite.
alignment bioinformatics cpp hh-suite hhblits hhpred hhsearch opensource profile-profile-search profile-search protein-structure sequence-search simd viterbi
Last synced: 14 Apr 2025
https://github.com/soedinglab/metaeuk
MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
bioinformatics eukaryotes gene-discovery gene-prediction metagenomics
Last synced: 26 Jul 2025
https://github.com/soedinglab/plass
sensitive and precise assembly of short sequencing reads
bioinformatics metagenomics metatranscriptomics opensource proteins proteomics sequence-assembler
Last synced: 04 Apr 2025
https://github.com/soedinglab/ccmpred
Protein Residue-Residue Contacts from Correlated Mutations predicted quickly and accurately.
Last synced: 27 Apr 2025
https://github.com/soedinglab/CCMpred
Protein Residue-Residue Contacts from Correlated Mutations predicted quickly and accurately.
Last synced: 09 May 2025
https://github.com/soedinglab/spacedust
Discovery of conserved gene clusters in multiple genomes
Last synced: 27 Apr 2025
https://github.com/soedinglab/mmseqs2-app
MMseqs2 app to run on your workstation or servers
alphafold2 bioinformatics colabfold docker docker-compose electron foldseek golang mmseqs profile-search sequence-search structure-search vue
Last synced: 06 Apr 2025
https://github.com/soedinglab/WIsH
Predict prokaryotic host for phage metagenomic sequences
Last synced: 23 Mar 2025
https://github.com/soedinglab/wish
Predict prokaryotic host for phage metagenomic sequences
Last synced: 27 Apr 2025
https://github.com/soedinglab/spacepharer
SpacePHARER CRISPR Spacer Phage-Host pAiRs findER
bioinformatics crispr host-pathogen sequence-analysis
Last synced: 27 Apr 2025
https://github.com/soedinglab/prosstt
PRObabilistic Simulations of ScRNA-seq Tree-like Topologies
Last synced: 29 Jul 2025
https://github.com/soedinglab/pdbx
pdbx is a parser module in python for structures of the protein data bank in the mmcif format
Last synced: 22 Jul 2025
https://github.com/soedinglab/bammmotif
Bayesian Markov Model motif discovery - An expectation maximization algorithm for the de novo discovery of enriched motifs as modelled by higher-order Markov models.
Last synced: 27 Apr 2025
https://github.com/soedinglab/kclust
kClust is a fast and sensitive clustering method for the clustering of protein sequences. It is able to cluster large protein databases down to 20-30% sequence identity. kClust generates a clustering where each cluster is represented by its longest sequence (representative sequence).
Last synced: 27 Apr 2025
https://github.com/soedinglab/merlot
Reconstruct the lineage topology of a scRNA-seq differentiation dataset.
Last synced: 26 Feb 2025
https://github.com/soedinglab/b-lore
Bayesian multiple logistic regression for GWAS meta-analysis
Last synced: 10 Oct 2025
https://github.com/soedinglab/transannot
TransAnnot - a fast transcriptome annotation pipeline
annotation assembly bioinformatics bioinformatics-pipeline transcriptomics
Last synced: 27 Apr 2025
https://github.com/soedinglab/mmseqs
alignment cpp mmseqs opensource sequence-clustering
Last synced: 27 Apr 2025
https://github.com/soedinglab/bammmotif2
Bayesian Markov Model motif discovery tool version 2 - An expectation maximization algorithm for the de novo discovery of enriched motifs as modelled by higher-order Markov models.
bioinformatics chip-seq motif-analysis motif-discovery ngs-analysis
Last synced: 27 Apr 2025
https://github.com/soedinglab/tejaas
Tejaas - a tool for discovering trans-eQTLs
eqtl eqtl-mapping gene-expression gtex reverse-regression trans-eqtl
Last synced: 27 Apr 2025
https://github.com/soedinglab/peng-motif
PEnG-motif is an open-source software package for searching statistically overrepresented motifs (position specific weight matrices, PWMs) in a set of DNA sequences.
bioinformatics chip-seq dna motif-discovery rna
Last synced: 27 Apr 2025
https://github.com/soedinglab/bbcontacts
Prediction of beta-strand pairing from direct coupling patterns
Last synced: 03 Aug 2025
https://github.com/soedinglab/hhdatabase_cif70
Scripts to generate the pdb70 database for hh-suite on the basis of pdb's mmcif format
Last synced: 27 Apr 2025
https://github.com/soedinglab/bamm_webserver
Webserver for motif discovery with higher-order Bayesian Markov Models (BaMMs)
bamms bioinformatics motif-discovery webserver
Last synced: 02 Sep 2025
https://github.com/soedinglab/bamm-suite
De-novo motif discovery and optimization
Last synced: 17 Jul 2025
https://github.com/soedinglab/ccmgen-scripts
Contains plotting scripts, examples, and other small scripts relevant to CCMgen and the corresponding publication.
Last synced: 16 May 2026
https://github.com/soedinglab/prosstt-r
An R package with evaluation and visualization functions for the python PROSSTT package
Last synced: 06 Mar 2026
https://github.com/soedinglab/bipartite_motif_finder
BMF: Bipartite Motif Finder
Last synced: 04 Oct 2025
https://github.com/soedinglab/xxmotif
XXmotif: eXhaustive, weight matriX-based motif discovery in nucleotide sequences
bioinformatics motif-discovery
Last synced: 15 May 2026
https://github.com/soedinglab/mmseqs2-regression
MMseqs2 Regression Testing
Last synced: 27 Apr 2025
https://github.com/soedinglab/bmf-webserver
Web server for Bipartite Motif Finder (BMF)
Last synced: 15 May 2026
https://github.com/soedinglab/contactpred-felsenstein
Felsenstein implementation for phylogeny correction
Last synced: 21 Nov 2025
https://github.com/soedinglab/hhdatabase_pfam
Scripts to generate the pfam database for hh-suite
Last synced: 11 Apr 2026
https://github.com/soedinglab/hhdatabase_scop
Build scripts for the scop databases for hh-suite
Last synced: 19 Nov 2025
https://github.com/soedinglab/bamm-benchmark
Scripts and data for generating the benchmarks in the W Ge, et al. paper.
Last synced: 16 Jul 2025
https://github.com/soedinglab/bmf-paper
Notebooks to reproduce the analyses in BMF manuscript
Last synced: 18 Sep 2025
https://github.com/soedinglab/degradation_scripts
data analysis scripts for degradation pathway story
Last synced: 26 Feb 2025
https://github.com/soedinglab/merlot-scripts
Benchmark and plotting scripts for the MERLoT paper
Last synced: 28 Jul 2025
https://github.com/soedinglab/metaeuk-regression
Regression test suite for MetaEuk
Last synced: 27 Jul 2025
https://github.com/soedinglab/snptarget
A statistical approach to predict enhancer-gene interactions
Last synced: 13 Oct 2025
https://github.com/soedinglab/art_marzooplclk
Accompanying repository for the publication "RNA sequencing indicates widespread conservation of circadian clocks in marine zooplankton"
Last synced: 17 Sep 2025
https://github.com/soedinglab/csgraph_mod
Modification of the scipy csgraph class to allow tracking of the visited nodes
Last synced: 21 Jun 2025