I am running a command to create a tree using the raxml-rapid-bootstrap pipeline available in the tutorial. When I run the command it generates a warning message: Found 139 sequences that are exactly identical to other sequences in the alignment , and provides an alternate file without duplicate sequences. My questions:
Can I continue with this command, even with the duplicate sequences? (it is still running)
How do I use the alternate file (given in fasta format) ?
Here is the command I had run:
qiime phylogeny raxml-rapid-bootstrap
–p-seed 1723 **
–o-tree Clinical/raxml-cat-bootstrap-tree.qza \