Tree And MSA Not Aligning As Expected

[g12342jn]

Hello,

It looks like the tree tips and sequences are not aligning as expected:

Here is the file contents:

>art
artartartartarta
>bart
bartbartbartbart
>cady
cadycadycadycady
>daak
daakdaakdaakdaak
>gary
garygarygarygary
>ham
hamhamhamhamhamh
>kart
kartkartkartkart
>mary
marymarymarymary
>naat
naatnaatnaatnaat
>rant
rantrantrantrant
(art,((((gary,daak),(cady,bart)),(ham,((kart,(mary,(rant,naat))))))));

Thanks,
Greg

[stephenshank]

Dear @g12342jn,

Thanks for posting this issue. Two things:

1. Mary is capitalized in the FASTA but lower cased mary in the Newick, which could cause discrepancies. The code is not very fault tolerant.
2. Your tree contains spurious internal nodes, emphasized in red below:
   

visualized at phylotree.hyphy.org which you may find useful. Here is one that does not:

(art,(((gary,daak),(cady,bart)),(ham,(kart,(mary,(rant,naat))))));

Nevertheless, fixing these did not resolve the issue. The suspected line is:

alignment.js/src/helpers/jointSort.js

Line 22 in 978bcda

const ordered_leaf_names = tree.getTips().map(d => d.data.name);

which attempts to get a linear ordering of the nodes as they appear when the tree is laid out. This appears to work for the advertised CD2 example but not for your toy dataset. I'll need to do a bit more digging to understand why.

Best,
Stephen

[g12342jn]

Hello Stephen,

Thanks for getting back to me.
The capital was due to Mac OS "auto capitalization on a new line feature", it is not in the file. T_T
I should have caught that before I entered the comment, sorry for the confusion.
I attached the sample file for your reference:
art_bart.txt

Edit: I needed to rename the file to .txt in order to import to the comments here, not that it should matter, but I thought that I should mention.

Your assistance is much appreciated.

Regards,
Greg

[stephenshank]

Dear @g12342jn,

Just a quick update. I've architected a fix, but it will involve some slight refactoring of the react-phylotree dependency.

I hope to do a patch release to both packages by the end of the week, and will follow up then.

This issue uncovered some subtle flaws in existing logic, so it is greatly appreciated!

Best,
Stephen

[g12342jn]

Stephen,

That is great news!

Thank you for looking into this.

I will keep an eye out for your follow up message.

Regards,
Greg