deyuanyang's repositories
jcvi
Python library to facilitate genome assembly, annotation, and comparative genomics
orthoflow
Orthoflow is a workflow for phylogenetic inference of genome-scale datasets of protein-coding genes.
barcode-constrained-phylogeny
Pipeline for building topologically-constrained phylogenies from DNA barcode data
taxonworks
Workbench for biodiversity informatics.
fastHaN
fastHaN is a fast and scalable program for constructing haplotype networks for large samples
RyanLabShortReadAssembly
Our pipeline for assembling short reads
gnfinder
GNfinder finds scientific names in UTF8 texts, PDF files, MS Word/Excel documents, URLs etc.
mtGrasp
mtGrasp: Snakemake pipeline for de novo reference-grade mitochondrial genome assembly and standardization
skim2phylo
A snakemake pipeline for the batch assembly, annotation, and phylogenetic analysis of mitochondrial genomes and ribosomal genes from genome skims
teaching
Tutorials written for my Spring 2015 class on the basics of computing for biologists
genome_skimming_LAB
A set of scripts to analyze Illumina sequencing data to find whole mitochondrial genomes using Smithsonian's Hydra HPC
mito
The mitosheet package, trymito.io, and other public Mito code.
samtools
Tools (written in C using htslib) for manipulating next-generation sequencing data
MAVR
various bioinformatic instruments
FastaChar
A tool to determine molecular diagnostic characters for species from sequences in fasta format
SPdel
Comparing species delimitation methods and statistics for DNA Barcoding data sets
pyGenomeViz
A genome visualization python package for comparative genomics
graphphylo
visualization of phylogenetic output files
Mitochondrial-ORFans
This repository serves as a resource for the scripts and data associated with our research article "ORFans in Mitochondrial Genomes of Marine Polychaete Polydora"
CandiHap
A haplotype analysis toolkit for natural variation study.
Mitochondrial_Benchmarking_study
This repository contains the codes and additional data utilized in the benchmark study of short read based mitochondrial assemblers for human datasets
ugene
UGENE is free open-source cross-platform bioinformatics software
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.
bold_identification
To identify taxa of given sequences via BOLD system (http://www.boldsystems.org/index.php)
delineate
Package for species delimitation analysis
Mito-AssemblyViz
Mitochondrial Genome Assembly Assessment Visualization
ML-Pipeline
Scripts for Shiu Lab Machine Learning - primarily using SK-Learn