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github.com/broadinstitute/viral-pipelines/augur_from_mltree

integration_instructionsResearch softwarekeyboard_double_arrow_right Software 08 Apr 2025Publisher:Zenodo
Authors: Broad Viral Genomics;

doi: 10.5281/zenodo.18473361 , 10.5281/zenodo.18506631 , 10.5281/zenodo.15428517 , 10.5281/zenodo.18869943 , 10.5281/zenodo.15177572 , 10.5281/zenodo.18054043 , 10.5281/zenodo.18674058 , 10.5281/zenodo.18634689 , 10.5281/zenodo.15177571 , 10.5281/zenodo.18236325 , 10.5281/zenodo.18774914

github.com/broadinstitute/viral-pipelines/augur_from_mltree

Abstract

Take a premade maximum likelihood tree (Newick format) and run the remainder of the augur pipeline (timetree modificaitons, ancestral inference, etc) and convert to json representation suitable for Nextstrain visualization. See https://nextstrain.org/docs/getting-started/ and https://nextstrain-augur.readthedocs.io/en/stable/

  • BIP!
    Impact byBIP!
    selected citations
    These citations are derived from selected sources.
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    		 0
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    		 Average
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    		 Average
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    		 Average
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average