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Good morning! I am trying to use Phylophoenix and the files produced in the output folder do not seem to match the readme. I do see a newick file produced, but I do not know how the distances were computed, as the snp matrix i get in SNVPhyl_GRiPHin_Summary.xlsx is on a completely different scale. Can someone point me to documentation or tell me how the tree in the newick file was computed?

Hi, <@U0C4EFD1G0N>!

Slack uses _channels_ to organise discussions. Press the _`...` more_ option on the left sidebar. Then hover over _Your organisation_, and finally select _Channels_ to browse.

Each nf-core pipeline has it’s own channel (e.g. <#CE8SSJV3N>). Please post any questions about specific pipelines in the relevant channel.

If you’re not sure where to post your message, please ask <@UE4L64T4G> for help.

I can usually guess which pipeline people are talking about, but I have no idea here sorry :sweat_smile:

Ah, found a module with `newick` in the name - <#C04NLA7QHH9> or <#CEA7TBJGJ> maybe?

Try those channels :point_up_2::skin-tone-2:

thank you for getting back to me <@UE4L64T4G>

i am referring to this project: <https://github.com/CDCgov/phylophoenix|github.com/CDCgov/phylophoenix>

believe it or not it has a link that points to this slack workspace

is there a chance you would know someone who would know how to get Phylophoenix working?

hah, fun - looks like they've used the nf-core pipeline template (that comes with that link, on the assumption that an nf-core pipeline will have such a channel) and they never removed it from the readme.

This is not an nf-core pipeline so this slack isn't really the place to go sorry. Best bet is likely the github issues and/or github wiki that they have for the pipeline.

Looks like <@U037FMACF8V> and <@U02NDMTLTCY> are in this slack though, so might be able to help?