Although I provided 10 sequences, only two of them were clustered. What happened to the other 8 sequences?

[Y-antian]

my input:

my cluster:

[Y-antian]

It appears that the multiPrime function only utilizes the portion of the ID before the "-" symbol.

[joybio]

Yes, that's correct. The new updated version of multiPrime does not permit the use of colons (:), hyphens (-), or spaces in the FASTA IDs. If any of these characters exist, only the first element before these separators will be considered as the ID.