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Update description #267

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Aug 13, 2024
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Update description #267

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description: Update GitHub URLs
joverlee521 Aug 9, 2024
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description: Add link to clade I build
joverlee521 Aug 9, 2024
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4 changes: 3 additions & 1 deletion phylogenetic/defaults/description.md
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We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequences and metadata for sharing their work. Please note that although data generators have generously shared data in an open fashion, that does not mean there should be free license to publish on this data. Data generators should be cited where possible and collaborations should be sought in some circumstances. Please try to avoid scooping someone else's work. Reach out if uncertain.

We maintain three views of MPXV evolution:
We maintain four views of MPXV evolution:

The first is [`mpox/lineage-B.1`](https://nextstrain.org/mpox/lineage-B.1), which focuses on lineage B.1 of the global outbreak that started in 2022 and includes as many sequences as possible. Here, we conduct a molecular clock analysis in which evolutionary rate is estimated from the data (with a resulting estimate of ~6 &times; 10<sup>-5</sup> subs per site per year).

The second is [`mpox/clade-IIb`](https://nextstrain.org/mpox/clade-IIb), which focuses on recent viruses transmitting from human-to-human and includes viruses belonging to clade IIb. All good quality sequences that are not lineage B.1 are included, while lineage B.1 sequences is heavily subsampled to allow non-B.1 diversity to be studied.Here, we also conduct a molecular clock analysis in which evolutionary rate is estimated from the data (with a resulting estimate of ~6 &times; 10<sup>-5</sup> subs per site per year).

The third is [`mpox/all-clades`](https://nextstrain.org/mpox/all-clades), which focuses on broader viral diversity and includes viruses from the animal reservoir and previous human outbreaks, encompassing clades I, IIa and IIb as described in [Happi et al](https://doi.org/10.1371/journal.pbio.3001769) and endorsed by a [WHO convened consultation](https://worldhealthorganization.cmail20.com/t/ViewEmail/d/422BD62D623B6A3D2540EF23F30FEDED/F75AF81C90108C72B4B1B1F623478121?alternativeLink=False).

The fourth is [`mpox/clade-I`](https://nextstrain.org/mpox/clade-I), which focuses on clade I sequences and includes as many sequences as possible.
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@jameshadfield Feel free to update this if there is more you would like to add about the clade I build.

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Looks good, thanks!


#### Analysis
Our bioinformatic processing workflow can be found at [github.com/nextstrain/mpox](https://github.com/nextstrain/mpox) and includes:
- sequence alignment by [nextalign](https://docs.nextstrain.org/projects/nextclade/en/stable/user/nextalign-cli.html)
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