Question: Bootstrapping a phylogenetic tree using FastTree
0
gravatar for ginohino
3 months ago by
ginohino0
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:

GCA_123456000

GCA_123456001

Becomes:

GCA_123456

GCA_123456

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!

Thanks!

ADD COMMENTlink written 3 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 3 months ago by a.zielezinski8.7k
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