Bootstrapping a phylogenetic tree using FastTree

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Entering edit mode

5.7 years ago

ginohino • 0

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

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!

fasttree bootstrapping replicates phylogenetics • 4.6k views

ADD COMMENT • link 5.7 years ago by ginohino • 0

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

ADD REPLY • link 5.7 years ago by Andrzej Zielezinski 11k

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