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mitowrap

A snakemake pipeline wrapping MitoZ and getOrganelle for de novo mitogenome assembly using short reads and subsequent QC.

ml-pipeline

Scripts for Shiu Lab Machine Learning - primarily using SK-Learn

mt-genome

Perl scripts for large-scale analyses of mitochondrial genomes

mtgrasp

mtGrasp: Snakemake pipeline for de novo reference-grade mitochondrial genome assembly and standardization

orthoflow

Orthoflow is a workflow for phylogenetic inference of genome-scale datasets of protein-coding genes.

phylomito

A python script for mitochondrial supermatrix phylogenomics.

polychate_mt

pycoistats

A collection of scripts to manage COI data, calculate pairwise distances and plot them

pygenomeviz

A genome visualization python package for comparative genomics

python_bioinfo

Several scripts for basic bioinformatics data manipulation

ray

Ray is a unified framework for scaling AI and Python applications. Ray consists of a core distributed runtime and a toolkit of libraries (Ray AIR) for accelerating ML workloads.

ryanlabshortreadassembly

Our pipeline for assembling short reads

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

skim2phylo

A snakemake pipeline for the batch assembly, annotation, and phylogenetic analysis of mitochondrial genomes and ribosomal genes from genome skims

spdel

Comparing species delimitation methods and statistics for DNA Barcoding data sets

speciesdistributionmaps

Script that pulls data from a local postgresql database and plots lat long data on a map

taxonworks

Workbench for biodiversity informatics.

travisia-chinensis-and-travisia-amoyensis

ugene

UGENE is free open-source cross-platform bioinformatics software