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barcode-constrained-phylogeny

Pipeline for building topologically-constrained phylogenies from DNA barcode data

bioinformatic_algorithms_coding_challenges

Scripts for the coding challenges of the course "Bioinformatic algorithms: an active learning approach"

bioinformatics-pipeline

Courses, tutorials and books that facilitate bioinformatics.

biopython-cn

Biopython Tutorial Chinese Translation

bold_identification

To identify taxa of given sequences via BOLD system (http://www.boldsystems.org/index.php)

c-c-

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candihap

A haplotype analysis toolkit for natural variation study.

connor

Deduplication based on custom inline DNA barcodes.

coretracker

CoreTracker, a codon reassignment tracker

deeplearningancientdna

Here I show how to use Convolutional Neural Networks (CNNs) for Ancient DNA analysis

delineate

Package for species delimitation analysis

fasta_tools

This package contains Perl programs/scripts that perform frequently needed operations on FASTA format files.

fastachar

A tool to determine molecular diagnostic characters for species from sequences in fasta format

fasthan

fastHaN is a fast and scalable program for constructing haplotype networks for large samples

genome_skimming_lab

A set of scripts to analyze Illumina sequencing data to find whole mitochondrial genomes using Smithsonian's Hydra HPC

getorganelledb

GetOrganelle Default Databases

gnfinder

GNfinder finds scientific names in UTF8 texts, PDF files, MS Word/Excel documents, URLs etc.

graphphylo

visualization of phylogenetic output files

group_genetic_distance

To derive within- and between-groups genetic distance based on pairwise genetic distance matrix

insect_genome_assemblies

scripts used to download and analyze insect assemblies from GenBank

jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics

karaj

mavr

various bioinformatic instruments

metal

Alignment Distance Metrics

mito

The mitosheet package, trymito.io, and other public Mito code.

mito-assemblyviz

Mitochondrial Genome Assembly Assessment Visualization

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"

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

mitochondrialgeneanalysis

mitos2_wrapper

Wrapper for MITOS2 annotation tool - generates a .gbk file from plain fasta sequences