The number of taxa in the generated tree is smaller than the number of input taxa

[nimua]

Hi, There are 334 taxa in my input data, but udance.maxqs.nwk only contains about 270 taxa. I don't understand the reason for the decrease in numbers.

udance.log

I used this config:

backbone: "de-novo" mainlines_config:

target number of taxa

n: 334

concatenation alignment length

length: 5000

[balabanmetin]

Species can be removed for several reasons such as QC, being a duplicate, or being unplaceable -- something we discussed in our manuscript. The good news is the unplaceable sequences can be replaced. Run a second iteration of udance and input your first output tree as the backbone tree. Does that make sense?

[nimua]

Thank you. That make sense.