diff --git a/phylogenetic/defaults/description.md b/phylogenetic/defaults/description.md index 558e663..29ae51f 100644 --- a/phylogenetic/defaults/description.md +++ b/phylogenetic/defaults/description.md @@ -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) @@ -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) ---