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Bioinformatics Workshop

We have curated our most popular Software & Data repositories so you can find them easily

After a gap in maintaining this page, we intend to resume posting periodic updates to highlight a variety of new resources as they become available. Our Lab's GitHub site also provides useful info and resources related to current projects.

New Featured Software: geographic coverage of DNA barcodes

7/15/2025

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Featured Software from the Kartzinel Lab: Geographic Coverage of DNA Barcodes. The inaugural code repository to be highlighted in our Featured Software section of the Software & Data page presents the Quarto Code Book published in association with our Molecular Ecology Review Paper, "Global Availability of Plant DNA Barcodes as Genomic Resources to Support Basic and Policy-Relevant Biodiversity Research" can be easily modified to evaluate the geographic coverage of other data sets. Although the featured code emphasizes geographic coverage from our work in Yellowstone National Park...

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Rolling out a curated set of software and data repositories

7/11/2025

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Over the past couple of years, a lot of things have changed. Some of those changes have brought improvements to the way we share the software and data that we generate in the lab, necessitated in part by the growing popularity of our work to a point that we recognized a substantial benefit to enhancing our commitment to easy access and open-source principles. 

To make it easier to find and access our most in-demand repositories -- often spread across a variety of platforms including GitHub, Zenodo, NCBI, BOLD, etc. -- we have created a main landing page on the website where we have curated a mix of both recent and timeless contributions to the field. Check it out!
Software & Data
You might also want to check out our lab's main GitHub repository, where we are increasingly making our projects publicly available so you can benefit from any updates we've made since posting a version of record for the code with a prior publication (e.g., a static record with a Zenodo DOI). 

I will periodically post updates to this blog in order to highlight and summarize important updates to help ensure the community is aware, but we will no longer be using these pages to share data or code directly as we have in the past.
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Simple phylogenetics workflow

3/26/2019

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On March 19th, Brian Gill kindly provided a broad overview of a phylogenetics workflow and resources. These are some great go-to documents for building simple phylogenies quickly, especially based on data from some of the common mitochondrial and chloroplast "DNA barcode" markers that we often use.

The workflow infographic to the right is simply out-of-the-ballpark outstanding.

A very valuable list of resources corresponding to each stage highlighted in this infographic follows below the break.

THANK YOU, Brian, for compiling this information.
Picture

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Dr. Tyler Kartzinel
Department of Ecology, Evolution, and Organismal Biology
Institute at Brown for Environment and Society
Brown University
​Address: 85 Waterman Street, Providence, Rhode Island 02912 USA
Office: 246(B)
​Lab (pre-PCR): 244
​Lab (post-PCR): 230
​Phone: 1-401-863-5851
tyler_kartzinel[at]brown.edu
Disclaimer: views expressed on this site are those of the author. They should not be interpreted as opinions or policies held by his employer, collaborators, or lab members. Mention of trade names or commercial products does not constitute endorsement.

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  • Home
  • Resources
    • Protocols
    • Software & Data
  • Work with us
    • Contract & Collaborate >
      • DNA metabarcoding
    • Join
  • Research
    • Publications
    • Yellowstone
    • Fray Jorge
    • Savanna Ecology
    • Molecular Parasitology
  • People
  • Conservation
  • Contact