I'm trying to bootstrap a tree using FastTree. The manual says to use SeqBoot to bootstrap the alignment I have, then use Fasttree with the -n option to instruct Fasttree the number of times my alignment has been replicated. The identifying headers outputted by SeqBoot are truncated (eg. GCA_123456789 to GCA_123456).
This header truncation results in duplicates in the alignment which cannot be read by Fasttree. In other words:
Which are now identical.
Does anyone know how to fix this problem? Should I even use the traditional way of bootstrapping a tree since Fasttree does already do a 'quick' bootstrapping by default?
If I'm incorrect in my understanding, please let me know, I'm new to this!