Yatish Turakhia comments

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                                            Yatish Turakhia

matOptimize crashes when samples are numerically named

@yceh This should be an easy fix. We use "node_" for internal node naming now in UShER, which is what matOptimize should also do.

ENH: Add callback for discovered moves

@yceh Could you please help with this?

ENH: Display all maximally parsimonious locations in web interface, not just 1

Hi @corneliusroemer, have you tried the `--multiple-placements ` option in command line UShER?

ENH: Display all maximally parsimonious locations in web interface, not just 1

Adding @AngieHinrichs to see if she has any thoughts on adding this option to the web interface.

Not all nodes are shown in the tsv file generated by the function --translate

Adding @amkram who has developed matUtils summary --translate.

ENH: Speed up Usher webversion

Thanks for the feedback, @corneliusroemer. @AngieHinrichs are we using `usher-sampled-server` for the web version now? That should significantly speed up the tool by preloading the MAT and placing multiple samples...

Stop codons are chopped off in Auspice.json export, ORF8:Q27* wrongly displayed as ORF8:Q27

@amkram Please have a look. I think there should have been a "*" as @corneliusroemer points out.

Impute deletions as well as substitutions?

In a (distant) future version of UShER, we do plan to support insertions and deletions as well, but it's not happening soon, unfortunately. I am not aware of a different...

Usher not preserving the original tree topology

That's an unexpected behavior. Do you have a set of commands you can share for the two scenarios (preserved and changed topology)?

ENH: Make `sample type` an Auspice filter

@jmcbroome would this be easy to add?