Consider "iqtree -fast" instead of "FastTree"

Ecogenomics / GTDBTk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

https://ecogenomics.github.io/GTDBTk/

GNU General Public License v3.0

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Consider "iqtree -fast" instead of "FastTree" #179

Closed tseemann closed 4 years ago

tseemann commented 5 years ago

http://www.iqtree.org/doc/Command-Reference

-fast 
Turn on the fast tree search mode, where IQ-TREE will just construct two starting trees:
maximum parsimony and BIONJ, which are then optimized by nearest neighbor interchange
(NNI). Introduced in version 1.6.

Author says it is more accurate for same speed.

donovan-h-parks commented 4 years ago

Our evaluation indicated IQ-Tree -fast and FastTree deviate from IQ-Tree to the same extent. In all cases, known challenging taxa were not always inferred to be monophyletic. We have decided to stay with FastTree for now since we are more familiar with its limitations, but will continue to evaluate other options.