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phylogenetic: Update description.md for Nextclade v3
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Remove reference to nextalign and update available files to match
the output files from Nextclade v3.
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joverlee521 committed Oct 18, 2024
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6 changes: 3 additions & 3 deletions phylogenetic/defaults/description.md
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Expand Up @@ -12,7 +12,7 @@ The fourth is [`mpox/clade-I`](https://nextstrain.org/mpox/clade-I), which focus

#### 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)
- sequence alignment by [Nextclade](https://docs.nextstrain.org/projects/nextclade/en/stable/user/nextclade-cli/index.html)
- masking several regions of the genome, including the first 1350 and last 6422 base pairs and multiple repetitive regions of variable length
- phylogenetic reconstruction using [IQTREE-2](http://www.iqtree.org/)
- ancestral state reconstruction and temporal inference using [TreeTime](https://github.com/neherlab/treetime)
Expand All @@ -26,9 +26,9 @@ Curated sequences and metadata are available as flat files at:
- [data.nextstrain.org/files/workflows/mpox/sequences.fasta.xz](https://data.nextstrain.org/files/workflows/mpox/sequences.fasta.xz)
- [data.nextstrain.org/files/workflows/mpox/metadata.tsv.gz](https://data.nextstrain.org/files/workflows/mpox/metadata.tsv.gz)

Pairwise alignments with [Nextclade](https://clades.nextstrain.org/) against the [reference sequence MPXV-M5312_HM12_Rivers](https://www.ncbi.nlm.nih.gov/nuccore/NC_063383), insertions relative to the reference, and translated ORFs are available at
Pairwise alignments with [Nextclade](https://clades.nextstrain.org/) against the [reference sequence MPXV-M5312_HM12_Rivers](https://www.ncbi.nlm.nih.gov/nuccore/NC_063383), Nextclade analysis results, and translated ORFs are available at
- [data.nextstrain.org/files/workflows/mpox/alignment.fasta.xz](https://data.nextstrain.org/files/workflows/mpox/alignment.fasta.xz)
- [data.nextstrain.org/files/workflows/mpox/insertions.csv.gz](https://data.nextstrain.org/files/workflows/mpox/insertions.csv.gz)
- [data.nextstrain.org/files/workflows/mpox/nextclade.tsv.zst](https://data.nextstrain.org/files/workflows/mpox/nextclade.tsv.zst)
- [data.nextstrain.org/files/workflows/mpox/translations.zip](https://data.nextstrain.org/files/workflows/mpox/translations.zip)

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