Sequedex places DNA on the Tree of Life
Sequedex recognizes ATG (protein start) in DNA sequence
Vertical axis is the number of reads assigned; horizontal axis is the location on the phylogenetic tree of viruses.
Functional rollups show significant differences in gene frequencies transcripome of an organism that has not been its genome assembled.
Plot showing significant differences between groups; horizontal axis is phylogeny, vertical axis is function.  Red indicates significant decreases, blue indicates increases.
Plot showing discrimination among human tissue types by functional classification of transcriptome data.


Note: This website is currently undergoing revision for Sequedex Version 2. Until this is complete, content in some cases may be outdated or there may be broken links and/or other issues.


11 Dec 2018

Sequedex Version 2 released under BSD open source license.

09 Jun 2014

Version 1.0 released.

28 Sep 2012

Version 0.9.2 released.

17 Sep 2012

Site went live.

Download Sequedex

The current version is 2.1.1. The latest release can be downloaded from here or there.

Additional data modules may be downloaded from here.

Sequedex classifies DNA sequences:
Who they came from and What they do


  • Starting with version 2, Sequedex is open source
  • Analyzes collections of sequences in new ways, answering who is doing what? and bridging molecular to ecological scales of biology via evolution.
  • Extremely fast and resource-sparing. A single core of your laptop can be ~250,000X faster than BLAST and twice as fast as uploading your data to a cloud. Sequedex tames the data deluge that has been widely noted, bringing analysis costs back into line with sequencing costs without cloud security and outage issues.
  • Works for reads as short as 30 bp where other methods fail.  You don't have to distort your data through a non-linear filter like assembly just to get results. Linear and broad diagnostics enables ecological management strategies for tough problems.
  • Phylogenetic signature algorithm works for novel organisms, so you're not blind to microbes that aren't similar to those in genome databases. More sensitive to distant relationships than methods based on mapping methods.
  • We already built a Tree of Life for you, so your analysis doesn't have to wait on a team of bioinformaticians to finish their analysis first.


Potential applications for Sequedex exist anywhere analysis of biological sequences (bioinformatics) may be informative, including:

  • ID of infectious diseases whether arising from bacteria, parasites, or viruses (medical, public health, biodefense).
  • Characterizing gut, oral, and skin microbiomes of humans, livestock, and pets (medical, pharmaceutical, veterinary, consumer).
  • Metagenomics of soils, rivers, oceans, foods, and process environments. (ecology, manufacturing).
  • Transcriptome characterization (medical, pharmaceutical, agricultural, biofuels).
  • Enzyme mining (chemical manufacturing, biofuels).
  • Cancer genomics (medical, pharmaceutical).
  • Companion diagnostics (pharmaceutical, agricultural, consumer care).

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