not an issue, would like clarification on how to use pmsf

[vmkhot]

Hi there!

Task description I need to make ~15000 gene trees to use for a gene-tree-species-tree reconciliation (each with 10000 bootstraps). Genes have varying lengths and orthogroups have varying number of genes (4-1100)

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I would like to use mixture models to generate these trees - but it is computationally expensive. Instead I am opting to use the PMSF approximation but currently a little confused on the command line options in the reference manual.

I did some trials to see how the tree topology might change using a small orthogroup (see below)

What is the difference between using the model like -m LG+PMSF+G and -m LG+C60+G -ft <guide tree>? What does the command -m LG+PMSF+G do? and is it appropriate to use? Based on the other trees, using -m LG+C60+G -ft <guide tree> produces a totally different tree topology - which I'm inclined to say is incorrect?

Your help is greatly appreciated!

Thanks,

Varada

Using the model finder iqtree2 -s ../HOG_MSA/dir_57/N0.HOG0011294_MSA.faa -m MFP -madd LG+C20,LG+C60 -B 1000 -wbtl -T 30 --mem 10G

Using C60 mixture model iqtree2 -s ../../HOG_MSA/dir_57/N0.HOG0011294_MSA.faa -m LG+C60+G -mwopt -B 1000 -wbtl -T 30 --mem 10G -pre ./small_tree_C60/small_tree_C60

PMSF 1 iqtree2 -s ../../HOG_MSA/dir_57/N0.HOG0011294_MSA.faa -m LG+PMSF+G -mwopt -B 1000 -wbtl -T 30 --mem 10G -pre ./small_tree_pmsf

This didn't require me to add a guide tree

PMSF 2, using the previous C60 tree as the guide tree

iqtree2 -s ../../HOG_MSA/dir_57/N0.HOG0011294_MSA.faa -m LG+C60+G -ft ./small_tree_C60/small_tree_C60.treefile -mwopt -B 1000 -wbtl -T 30 --mem 10G -pre ./small_tree_pmsf/small_tree_pmsf_redo

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