DataMonkey Error Message: "- had 7747 sites"

[hannahg3009]

Hi! I'm a Master's Student using Aliview and DataMonkey to do my thesis, but I keep running into the same issue when I input my data into DataMonkey. Based on a set of instructions from a PhD student, I made a phylogenetic tree on 10k Trees and combined it in a file with my sequences from Aliview. I added other information based on the instructions like the number of characters, taxa, etc. I've already gone through and removed the stop codons, but I keep getting the same attached error message; this is my first time using any of these databases, so it's very likely I'm making a small mistake, but any help would be appreciated! I'm attaching the error message I keep getting and also my .txt file which includes my tree and my sequences. Thanks! analysis vdr.txt

[spond]

Dear @hannahg3009,

Are you able to export in anything other than NEXUS? I've come across a similar issue with another user before, and the problem is that this specific site generates broken NEXUS. For example,

1. The sequences in your alignment have 1281 characters each, but the NEXUS header declares NCHAR = 7686.
2. The block which tells you how to label the tree

   1 Papio_anubis,
   2 Pongo_abelli,
   3 Gorilla_gorilla_gorilla,
   4 Homo_sapiens,
   5 Pan_paniscus,
   6 Pan_troglodyytes_troglodytes;

Does not match the list of sequence names in the DATA block. I fixed the alignment for you, so you can submit to Datamonkey, but unless you are able to get valid NEXUS exported, you will have similar issues with other alignment.

Best, Sergei

vdr-fixed.txt