Sequences of interest pruned from input tree

[ncoots]

Hi @maclandrol,
I am having an issue while running CoreTracker.
I am getting the program to run successfully, however, I noticed that it consistently filters out the sequences of interest to me. I input sequences from at least 70 different species, but the only ones that appear to be missing from the output codon_data files are the ones that I care the most about. While running, CoreTracker tells me "DEBUG:root:Non-uniform sequence in sequences and tree. The tree will be pruned." So I'm assuming that my sequences of interest are pruned out. I would like to know what constitutes "non-uniform" and if there is a way that I can keep them from being removed? I'm aware that those sequences are particularly divergent from the rest...which is exactly why I want to use CoreTracker on them!

Thank you for your help,
Nicole

[maclandrol]

Hello @ncoots, this will mostly happen because your have species in your dna, protein sequence not in the phylogenetic tree. Make sure you are keeping the same names or that the species are in the phylogenetic tree (only species found in dna, protein and tree are kept).

If you are able to share your input data, I could have a look at that.

[ncoots]

Hello,
Thank you for your
output_p_aligned.txt
output.txt

response! I have checked and double-checked that the 4 species of interest are in all 3 datasets with the exact same name; however, 2 continue to be removed. I am attaching the 3 datasets here for you to look at. The two species that are consistently removed are "Acanthometra_sp" and "Lithomelissa_sp"

[maclandrol]

Indeed, they are present. Can you share the newick of the tree ? I will try to run it to check and get back to you as soon as I can.

[ncoots]

concat.tree.zip

Absolutely! Thanks!