pm-leung

pm-leung's Stars

• eco4cast/Statistical-Methods-Seminar-Series

  Repository for code shared be presenters in the EFI hosted Statistical Methods Seminar Series

  Language:HTML234107

• google-deepmind/alphafold3

  AlphaFold 3 inference pipeline.

  Language:Python5k555

• MrOlm/inStrain

  Bioinformatics program inStrain

  Language:Python14733

• rcedgar/reseek

  Protein structure alignment and search algorithm

  Language:C++393

• rcedgar/muscle

  Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.

  Language:C++21323

• nmatzke/3diphy

  Maximum likelihood structural phylogenetics by including Foldseek 3Di characters. Supporting Information for Puente-Lelievre et al. 2023n for

  Language:R183

• Nesvilab/FragPipe

  A cross-platform proteomics data analysis suite

  Language:Java20538

• google-deepmind/alphafold

  Open source code for AlphaFold 2.

  Language:Python12.9k2.3k

• michaelkyu/PlasX

  PlasX, a machine learning classifier for identifying plasmid sequences based on genetic architecture

  Language:Python291

• wandreopoulos/deeplasmid

  Language:Python172

• michaelkyu/MobMess

  Language:Python182

• jiarong/VirSorter2

  customizable pipeline to identify viral sequences from (meta)genomic data

  Language:Python22231

• xiezhq/ISEScan

  A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome

  Language:Python8416

• jhawkey/IS_mapper

  IS mapping software

  Language:Python5116

• thanhleviet/ISfinder-sequences

  Insertion sequences (Insertion Element) [https://en.wikipedia.org/wiki/Insertion_sequence] collected from ISfinder (https://isfinder.biotoul.fr/)

  6116

• bacpop/CELEBRIMBOR

  Core ELEment Bias Removal In Metagenome Binned ORthologs: A pipeline to make pangenomes from MAGs

  Language:Python22

• RosettaCommons/protein_generator

  Joint sequence and structure generation with RoseTTAFold sequence space diffusion

  Language:Python26543

• ml4bio/Dense-Homolog-Retrieval

  Nature Biotechnology: Ultra-fast, sensitive detection of protein remote homologs using deep dense retrieval

  Language:Python852

• Australian-Structural-Biology-Computing/website

  Use example theme to make website

  Language:HTML33

• morgannprice/fast.genomics

  Genome browser for thousands of representative bacteria and archaea

  Language:Perl9

• padlocbio/padloc

  Locate antiviral defence systems in prokaryotic genomes

  Language:R4810

• mdmparis/defense-finder

  Systematic search of all known anti-phage systems.

  Language:Python7713

• gbouras13/hybracter

  Automated long-read first bacterial genome assembly tool implemented in Snakemake using Snaketool.

  Language:Python1078

• husonlab/splitstree6

  SplitsTree App

  Language:Java986

• vdemichev/DiaNN

  DIA-NN - a universal automated software suite for DIA proteomics data analysis.

  Language:C++28253

• BenoitMorel/GeneRax

  Language:C++6811

• BenoitMorel/AleRax

  Gene tree - species tree reconciliation from gene tree distributions

  Language:C++193

• jedick/CHNOSZ

  Thermodynamic calculations and diagrams for geochemistry

  Language:R101

• sokrypton/ColabFold

  Making Protein folding accessible to all!

  Language:Jupyter Notebook2k496

• DessimozLab/fold_tree

  snakemake pipeline for creating trees from sequence sets

  Language:Jupyter Notebook695