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Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
Implementation of papers in 100 lines of code.
A versatile pairwise aligner for genomic and spliced nucleotide sequences
The toolbox used to deal with cactus whole genome alignments
Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.
FRACTAL: framework for distributed computing to trace large accurate lineages
🚦🧬 Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs
[AAAI'22] RepBin: Constraint-Based Graph Representation Learning for Metagenomic Binning
Implementations of SIMD instruction sets for systems which don't natively support them.
🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes
Scalable, Portable and Distributed Gradient Boosting (GBDT, GBRT or GBM) Library, for Python, R, Java, Scala, C++ and more. Runs on single machine, Hadoop, Spark, Dask, Flink and DataFlow
Methods for the analyses described in Álvarez-Carretero et al. 2022 (https://doi.org/10.1038/s41586-021-04341-1)
Generalizing Phylogenetic Posterior Estimator from MCMC samples via subplit Bayesian networks
[NeurIPS'22] Graph Coloring via Neural Networks for Haplotype Phasing of Polyploid Species and Viral Quasispecies
Benchmark empirical datasets for phylogenetic method development
Efficient phylogenomic software by maximum likelihood
Active Segmentation Project
🧑🏫 60+ Implementations/tutorials of deep learning papers with side-by-side notes 📝; including transformers (original, xl, switch, feedback, vit, ...), optimizers (adam, adabelief, sophia, ...), ga…
Graph Attention Networks (https://arxiv.org/abs/1710.10903)
Transformers for Information Retrieval, Text Classification, NER, QA, Language Modelling, Language Generation, T5, Multi-Modal, and Conversational AI
A PyTorch Implementation of Matrix Capsules with EM Routing