wwood

Ben J Woodcroft's starred repositories

croc

Easily and securely send things from one computer to another :crocodile: :package:

scalene

Scalene: a high-performance, high-precision CPU, GPU, and memory profiler for Python with AI-powered optimization proposals

Language:PythonApache-2.011435 90 459

TiddlyDesktop

A custom desktop browser for TiddlyWiki 5 and TiddlyWiki Classic, based on nw.js

Language:JavaScript1636 82 261

rust-bio

This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.

Language:RustMIT1548 71 196

diamond

Accelerated BLAST compatible local sequence aligner.

Language:C++GPL-3.01003 36 690

scikit-bio

scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

Language:PythonBSD-3-Clause873 52 1019

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.

Language:CythonMIT769 48 912

vsearch

Versatile open-source tool for microbiome analysis

Language:C++NOASSERTION650 44 532

hh-suite

Remote protein homology detection suite.

Language:CGPL-3.0517 25 322

Krona

Interactively explore metagenomes and more from a web browser.

Language:JavaScript459 39 177

Jellyfish

A fast multi-threaded k-mer counter

Language:C++NOASSERTION455 30 182

vegan

R package for community ecologists: popular ordination methods, ecological null models & diversity analysis

Language:RGPL-2.0437 37 440

Mash

Fast genome and metagenome distance estimation using MinHash

Language:C++NOASSERTION381 33 165

rust-htslib

This library provides HTSlib bindings and a high level Rust API for reading and writing BAM files.

Language:RustMIT291 29 155

parasail

Pairwise Sequence Alignment Library

Language:CNOASSERTION240 18 94

DendroPy

A Python library for phylogenetic scripting, simulation, data processing and manipulation.

Language:PythonNOASSERTION204 13 134

pulp

Language:RustMIT176 8 2

CheckM2

Assessing the quality of metagenome-derived genome bins using machine learning

Language:ScilabGPL-3.0159 9 99

agc

Assembled Genomes Compressor

Language:C++MIT150 7 13

pharokka

fast phage annotation program

Language:PythonMIT139 9 98

seqmagick

An imagemagick-like frontend to Biopython SeqIO

Language:PythonGPL-3.0108 12 76

enrichM

Toolbox for comparative genomics of MAGs

Language:Python80 7 67

Lorikeet

Strain resolver for metagenomics

Language:RustAGPL-3.066 5 9

gappa

A toolkit for analyzing and visualizing phylogenetic (placement) data

Language:C++GPL-3.057 7 28

ALE

Amalgamated likelihood estimation (ALE) is a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (cf. http://arxiv.org/abs/1211.4606 ), which allows for the duplication, transfer and loss of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees.

Language:C++44 7 35