This release contains changes for datasets:
- Mpox virus (All clades) (nextstrain/mpox/all-clades)
- Mpox virus (Clade I) (nextstrain/mpox/clade-i)
- Mpox virus (Clade IIb) (nextstrain/mpox/clade-iib)
- Mpox virus (Lineage B.1) (nextstrain/mpox/lineage-b.1)
- Human Metapneumovirus (nextstrain/hmpv/all-clades/NC_039199)
Mpox virus (All clades) (nextstrain/mpox/all-clades)
- Newly released sequences are included.
- Sequences are now downloaded from Pathoplexus instead of NCBI virus. This allows inclusion of restricted-use clade I sequences from INRB (Placide Mbala-Kingebeni's group) in the DRC. This nearly doubles clade I sequences available.
- Based on user feedback, the QC rule for missing data (Ns) has been made more lenient.
- Masked ranges that are ignored for placement have been updated.
Mpox virus (Clade I) (nextstrain/mpox/clade-i)
- Newly released sequences are included.
- Sequences are now downloaded from Pathoplexus instead of NCBI virus. This allows inclusion of restricted-use clade I sequences from INRB (Placide Mbala-Kingebeni's group) in the DRC. This nearly doubles clade I sequences available.
- Based on user feedback, the QC rule for missing data (Ns) has been made more lenient.
- Masked ranges that are ignored for placement have been updated.
Mpox virus (Clade IIb) (nextstrain/mpox/clade-iib)
- Newly released sequences are included.
- Sequences are now downloaded from Pathoplexus instead of NCBI virus. This allows inclusion of restricted-use clade I sequences from INRB (Placide Mbala-Kingebeni's group) in the DRC. This nearly doubles clade I sequences available.
- Based on user feedback, the QC rule for missing data (Ns) has been made more lenient.
- Masked ranges that are ignored for placement have been updated.
Mpox virus (Lineage B.1) (nextstrain/mpox/lineage-b.1)
- Newly released sequences are included.
- Sequences are now downloaded from Pathoplexus instead of NCBI virus. This allows inclusion of restricted-use clade I sequences from INRB (Placide Mbala-Kingebeni's group) in the DRC. This nearly doubles clade I sequences available.
- Based on user feedback, the QC rule for missing data (Ns) has been made more lenient.
- Masked ranges that are ignored for placement have been updated.
Human Metapneumovirus (nextstrain/hmpv/all-clades/NC_039199)
This release harmonizes the clade names to align with the proposal by Groen et al, 2023. The previous clade names are kept as "Alt. clade" to allow linking back to previous results.