Question: Bootstrapping a phylogenetic tree using FastTree
gravatar for ginohino
14 months ago by
ginohino0 wrote:

Hi all,

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!


ADD COMMENTlink written 14 months ago by ginohino0

SeqBoot truncates sequence identifiers to first 9 characters. Open the alignment in a text editor and replace "GCA_" to empty string "".

ADD REPLYlink written 14 months ago by a.zielezinski9.1k
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