donovan-h-parks

Donovan H. Parks's repositories

CompareM

A toolbox for comparative genomics.

Language:PythonGPL-3.090 7 35

STAMP

Statistical Analysis of Metagenomic Profiles

Language:PythonGPL-3.090 14 43

RefineM

A toolbox for improving metagenome-assembled genomes.

Language:PythonGPL-3.062 5 52

Background-Subtraction-Library

C++ background substraction library

Language:C++GPL-3.045 80

PhyloRank

Assign taxonomic ranks based on evolutionary divergence.

Language:PythonGPL-3.02100

UniteM

Ensemble binning strategies for combining the output of multiple binning methods.

Language:PythonGPL-3.017 2 2

biolib

Python package for common tasks in bioinformatic.

Language:PythonGPL-3.013 2 3

GenomeTreeTk

A toolbox for working with genome trees.

Language:PythonGPL-3.010 2 3

ExpressBetaDiversity

Taxon- and phylogenetic-based beta diversity measures.

Language:C++GPL-3.06 2 7

FragmentClassificationPackage

Homology- and composition-based classifiers for assigning a taxonomic attribution to metagenomic fragments.

Language:C++500

pygmy

Visualization of large trees and associated metadata

Language:C++GPL-3.05 20

GeneTreeTk

A toolbox for working with gene trees.

Language:PythonGPL-3.0400

ANI-Cache

Cache-aware ANI calculations.

Language:PythonGPL-3.03 2 1

CommunityM

Identify, classify, and assemble 16S reads in metagenomic data.

Language:PythonGPL-3.03 20

Art

Generative art projects

Language:HTMLGPL-3.01 20

DBB

Bin scaffolds from a single metagenomic sample into population genomes.

Language:PythonGPL-3.01 2 2

DBSCAN

Clustering of sequences from environmental samples.

Language:C++1 30

DrawM

A toolkit for creating publication-quality images of phylogenetic trees.

Language:PythonGPL-3.01 2 3

GenomeTk

A toolbox for working with genome.

Language:PythonGPL-3.01 20

PETs

Putative Evolutionary Trees

Language:C++GPL-3.01 20

ViewM

Visualization of functional modules to aid biological interpretation of genomes.

GPL-3.01 20

advent-of-code

Solutions for Advent of Code

Language:PythonGPL-3.0000

finch-rs

A genomic minhashing implementation in Rust

Language:RustMIT000

LinkM

Finds links between 16S reads and assembled contigs.

GPL-3.0020

math-as-code

a cheat-sheet for mathematical notation in code form

MIT010

NCBI_ftp

python code for bioinformatics projects

Language:Python010

Prodigal

Prodigal Gene Prediction Software

Language:CGPL-3.0010

Roary

Rapid large-scale prokaryote pan genome analysis

Language:PerlNOASSERTION010

SketchM

Fast genome ANI estimation using k-mer sketches.

Language:RustGPL-3.0010

vega_templates

Python templates for creating visualizations using the Vega visualization grammar

GPL-3.0000