tomdstanton

Tom Stanton's starred repositories

noTunes

A simple macOS application that will prevent iTunes or Apple Music from launching.

Language:SwiftMIT3249 18 39

node2vec

Language:ScalaMIT2599 63 101

snap

Stanford Network Analysis Platform (SNAP) is a general purpose network analysis and graph mining library.

Language:C++NOASSERTION2153 177 169

RoseTTAFold

This package contains deep learning models and related scripts for RoseTTAFold

Language:PythonMIT1953 59 128

node2vec

Implementation of the node2vec algorithm.

Language:PythonMIT1194 20 92

localcolabfold

ColabFold on your local PC

Language:PythonMIT520 12 227

PHATE

PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.

Language:PythonGPL-2.0454 19 75

bifrost

Bifrost: Highly parallel construction and indexing of colored and compacted de Bruijn graphs

Language:C++BSD-2-Clause198 12 70

strobealign

Aligns short reads using dynamic seed size with strobemers

Language:C++MIT128 10 164

ncbi-acc-download

Download files from NCBI Entrez by accession

Language:PythonApache-2.0104 6 24

veryfasttree

Efficient phylogenetic tree inference for massive taxonomic datasets

Language:C++NOASSERTION96 14 21

minipileup

Simple pileup-based variant caller

Language:C79 4 13

ggPlantmap

Language:RMIT74 5 2

TreeSwift

TreeSwift: Fast tree module for Python 3

Language:PythonGPL-3.072 3 25

unikmer

A versatile toolkit for k-mers with taxonomic information

Language:GoMIT72 3 22

Integron_Finder

Bioinformatics tool to find integrons in bacterial genomes

Language:F*GPL-3.063 10 100

ska.rust

Split k-mer analysis – version 2

Language:RustApache-2.056 4 34

macsyfinder

MacSyFinder - Detection of macromolecular systems in protein datasets using systems modelling and similarity search.

Language:PythonGPL-3.046 10 69

mandrake

Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding

Language:PythonApache-2.036 6 23

PlasX

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

Language:PythonGPL-3.028 2 6

COPLA

A taxonomic classifier of plasmids

Language:PythonGPL-3.023 2 14

MrModeltest2

C program for selecting DNA substitution models using PAUP*

Language:C17 4 3

MobMess

Language:PythonGPL-3.015 2 6

rapidNJ

Fast implementation of the Neighbour-Joining method for phylogenetic inference

Language:C++GPL-2.013 1 6

riptide

Reaction Inclusion by Parsimony and Transcript Distribution

Language:PythonMIT11 3 9

bgc-pipeline

Language:Jupyter NotebookMIT9 7 2

pprodigal

Python3 wrapper for parallelized gene prediction using Prodigal

Language:PythonMIT8 2 3

pseudoR

Language:RMIT3 1 1

PASerotypeswitch

Workflow for detection of serotype switching by core genome alignment and insilico serotyping

Language:RGPL-3.02 10

pfaster

pneumococcal FASTA serotype calling

Language:PythonApache-2.02 20