Hi,
First of all, thank you for the great work on the tool and for the continuous improvements you make to it.
I have a question regarding the masking file updates that were introduced last week (https://github.com/nextstrain/mpox/blob/master/nextclade/resources/clade-i/mask.bed). We use the phylogenetic workflow from Nextstrain for our Mpox analyses, and I noticed that the masking files used by the phylogenetic pipeline for clade I (and the other clades) do not appear to have been updated.
Would you recommend continuing to use the existing masking files, or should we update them to the new masking BED files to obtain more accurate results?
Our analyses are performed on independent batches of samples, so we do not need phylogenetic consistency between different batches. However, we would like to ensure that we are using the most appropriate masking strategy for each analysis.
Could you clarify whether the new masking BED files should now be adopted in place of the previous ones for the phylogenetic workflow?
Thanks in advance for your guidance.
Hi,
First of all, thank you for the great work on the tool and for the continuous improvements you make to it.
I have a question regarding the masking file updates that were introduced last week (https://github.com/nextstrain/mpox/blob/master/nextclade/resources/clade-i/mask.bed). We use the phylogenetic workflow from Nextstrain for our Mpox analyses, and I noticed that the masking files used by the phylogenetic pipeline for clade I (and the other clades) do not appear to have been updated.
Would you recommend continuing to use the existing masking files, or should we update them to the new masking BED files to obtain more accurate results?
Our analyses are performed on independent batches of samples, so we do not need phylogenetic consistency between different batches. However, we would like to ensure that we are using the most appropriate masking strategy for each analysis.
Could you clarify whether the new masking BED files should now be adopted in place of the previous ones for the phylogenetic workflow?
Thanks in advance for your guidance.