Skip to main content

Lineage prediction from SARS-CoV-2 sequences

Project description


This is an experimental tool under development. The recommended method for calling lineages remains normal Pangolin:

A Re-engineered Method Allowing DetermInation of viraL LINeages

Armadillin is an experimental alternative approach to training models on lineages designated by the PANGO team.

Armadillin uses dense neural networks for assignment, which means it doesn't have to assume that positions with an N are the reference sequence. Armadillin is still very fast, in part because it sparsifies the feature input to this neural net during training.


With pipx (self-contained):

pip install --local pipx
pipx install  armadillin

or in your environment:

pip3 install armadillin


We'll use a NextStrain open sampled file for a demo:

armadillin sequences.fasta.xz


armadillin sequences.fasta.xz > output.tsv

If you have sequences already aligned to the reference you can make inference much faster using the --seqs_are_aligned parameter:

armadillin aligned.fasta.xz --seqs_are_aligned > output.tsv

Related tools

Pangolin is the OG for assigning lineages

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distributions

No source distribution files available for this release. See tutorial on generating distribution archives.

Built Distributions

armadillin-0.53-cp310-cp310-win_amd64.whl (88.5 kB view hashes)

Uploaded cp310

armadillin-0.53-cp310-cp310-win32.whl (76.6 kB view hashes)

Uploaded cp310

armadillin-0.53-cp39-cp39-win_amd64.whl (88.5 kB view hashes)

Uploaded cp39

armadillin-0.53-cp39-cp39-win32.whl (76.6 kB view hashes)

Uploaded cp39

armadillin-0.53-cp38-cp38-win_amd64.whl (88.4 kB view hashes)

Uploaded cp38

armadillin-0.53-cp38-cp38-win32.whl (76.5 kB view hashes)

Uploaded cp38

armadillin-0.53-cp37-cp37m-win_amd64.whl (87.4 kB view hashes)

Uploaded cp37

armadillin-0.53-cp37-cp37m-win32.whl (75.6 kB view hashes)

Uploaded cp37

armadillin-0.53-cp36-cp36m-win_amd64.whl (87.5 kB view hashes)

Uploaded cp36

armadillin-0.53-cp36-cp36m-win32.whl (75.6 kB view hashes)

Uploaded cp36

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Fastly Fastly CDN Google Google Object Storage and Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page