james hadfield

I ran into this error today (I think?) using augur version 17.1.0 (TreeTime version 0.9.2). In my case, the input tree (created using `augur tree`) had changed taxa names from...

Ahh - this is more complicated than I thought when we discussed it at last week's meeting! * Augur align can fill all gaps. [Looks like](https://github.com/search?q=org%3Anextstrain+%22--fill-gaps%22&type=code) we use this in...

> I see, what's the reason for that limitation? The way I've been thinking of auspice is like so: the unmodified auspice client is the tree viewer which certain other...

> Note that the PR review apps allow us to test on live nextstrain.org data That's true (and a big positive) but it doesn't help with local development and, some...

Revisiting this today, I think there are two different ways to expose the (command line) arguments: 1. `--mask-gaps {all, if-only-gaps, terminal}` and allow >1 values, e.g. `--mask-gaps if-only-gaps terminal` 2....

Update: I've implemented the ability to mask terminal gaps by reusing the code from https://github.com/nextstrain/ncov/blob/master/scripts/mask-alignment.py & added tests. This will allow our ncov pipeline to use `augur mask` again. The...

Hey @lauramataseje -- the number of bases on the presence/absence view is meaningless unfortunately [1], and I think we just assigned a fixed number of bases to each gene. Looking...

Hi @sabrinadiemert, I don't think so. Feel free to dive in if you can! Does the SVG reflect the zoomed-in view or is it also the default width?

> But I still would like to ask if there is any other way to color the branches in phandango. Hi @actledge - unfortunately this is not possible in phandango

You can see this clearly after commit 2ee049de718fb3ba7faed72b8ab9fb6dc40b4ed1 The background shading uses the same method as the red gubbins blocks do for finding the max and min y values for...