similar problem with PF2 spinning at 'Using a separate GTR+G model for each data block'

[shuiyin liu]

Hi Rob,

When I ran partitionfinder2 with two big datasets of 977 and 2821 genes, I met the similar problem with Teagan (in topoic "PF2 spinning at 'Using a separate GTR+G model for each data block'"). After over 20 days, it was still spinning at "Using a separate GTR+G model for each data block". Here is my command "python PartitionFinder.py RNA_977MOr2 --raxml --rcluster-max 100 -p 80", following the partitionfinder manual for big dataset. I noticed your response in last topic with iqtree2 as alternative analytical method. But the command "iqtree -s example.phy -p example.nex -m MFP+MERGE -rcluster 100" is the same as the greedy algorithm. Is there a good way to run partitionfinder in iqtree2 for big dataset, such as the rcluster algorithm with rcluster-max=100?

Best wishes

Shuiyin

[Rob Lanfear]

Hi Shuiyin,

The various ways to control clustering in IQ-TREE are listed here:

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

Just search for "rcluster".

Rob

[shuiyin liu]

Hi Rob,

Thank you! 

Best wishes

Shuiyin