Help with model selection, protein mixture models

[veronicamb]

Hello all,

I'm trying to use iqtree to find the best-fitting model for a protein dataset and I'd like to include Protein Mixture Models in the models considered.

Here's the command I used:

iqtree -s ../04_alignments/03_trimmed/06_informed/01_coding_NUC/01_AA
-pre Subset1_test2
-nt AUTO
-ntmax 40
-m MF
-mset WAG,LG,JTT
-msub nuclear
-madd C10,C20,C30,C40,C50,C60,LG4M,LG4X,CF4

However, the protein mixture models were not considered during the search. Can you help with what's missing in the command to fix it?

thank you!

Veronica

[roblanf]

@veronicamb here's one way to do what you want. I think the issue is that you have some competing demands in mset and madd, and -mset overrides -madd.

So, to fix that you can just put all the models you are interested in in -mset, like this:

iqtree2 -s test.fas -m MF -mset WAG,LG,JTT,C10,C20,C30,C40,C50,C60,LG4M,LG4X,CF4

• -m MF suppresses tree search
• -mset ... specifies the models to use in MF

Another tip - if you know you have 40 threads available, then I suggest just specifying all 40 for ModelFinder. It will usually be faster than -nt AUTO.

Just to note, I have to say that I too am wondering if we have a bug with -madd, because I can't make it behave as expected. We are working on this as we speak. The number of models has exploded in the last few years, so it's time for a re-organisation of how they are presented and analysed. In fact, we have working on this all afternoon today. Maybe @bqminh can put me straight on that though!

[veronicamb]

Thank you so much! This is a huge help. I'll try that right away.

Do you think there's a difference in the behavior of -madd in different versions of iqtree? I'm using 2.2.2

[roblanf]

There shouldn't be a difference. I tested with 2.3.4, but I have to say it didn't work as I thought it should. Best thing is to wait 24 hrs - we are meeting about this literally today. We are finalising MF2, and that requires some rationalisation of how models are presented.

[bqminh]

There is a bug that -madd is ignored (whereas IQ-TREE 1 works as expected). I don't know when this bug was "introduced", but @thomaskf will fix it. Thanks

[thomaskf]

@veronicamb I tested one protein dataset using the latest version, v2.3.4, with the exact command you used (except the number of CPU threads), and I found the option "-madd" should work. During the computation of the best model, the mixture models C20,C30,...,C60,LG4M,LG4X, and CF4 were considered. I am attaching a log file for your reference. As you can see, those mixture models were considered. Please feel free to let me know if you have any questions.
protein.phy.log

[veronicamb]

Thank you! I've been using iqtree 1, but I'll definitely give this a shot!

[veronicamb]

Will do! Thanks again

[000generic]

I have a similar question - and it looks like its not solved in protein.phy.log file posted above.

I'd like to use ModelFinder (-m MF) to identify the best fit model for thousands of gene alignments to then use for a species tree - providing a partition file including the ModelFinder best fit models per partition of the concatenated alignment for IQTree generation of the species tree - and in parallel generate gene trees by IQTree after model selection ( so actually run -MFP) for use in Asteroid generation of the species tree.

In doing this, I would like ModelFinder to consider the base models in IQTree (or even just the nuclear base models) - and 8 additional models I generated from a subset of the gene alignments using IQTree.

I would also like ModelFinder to consider mixture models C10, C20, and C60 - so for example, testing both the base model LG and LG combined with C20, LG+C20.

My command line is:

iqtree2 -m MF -madd C10,C20,C60 -s mollusca___4767at6447___subtree1.aa --prefix output/mollusca___4767at6447___subtree1 -mset Blosum62,Dayhoff,DCMut,EAL,ELM,JTT,JTTDCMut,LG,NQ.bird,NQ.insect,NQ.mammal,NQ.pfam,NQ.plant,NQ.yeast,Poisson,PMB,Q.bird,Q.insect,Q.mammal,Q.pfam,Q.plant,Q.yeast,VT,WAG,input/nQ.mollusca42_c50_s50_m1,input/nQ.mollusca42_c50_s50_m2,input/nQ.mollusca42_c50_s75_m1,input/nQ.mollusca42_c50_s75_m2,input/Q.mollusca42_c50_s50_m1,input/Q.mollusca42_c50_s50_m2,input/Q.mollusca42_c50_s75_m1,input/Q.mollusca42_c50_s75_m2 -mwopt -T 5 --threads-max 5 --symtest-remove-bad

I'm unclear from the discussion above if -mset still overrides -madd but it seems to do so in various output where I have been testing parameters in IQTree (version 2.3.6).

Currently, my solution in testing things is to add all combinations into -mset - so something like:

-mset LG,LG+C20

and not

-madd C20 -mset LG OR -mset LG,C20

I'm wondering if there is a more elegant way to do this - as its going to get ugly with so many base and mixture model combinations to consider.

More generally, I am wondering if I might be do something wrong in the design of my approach or command line.

Thank you very much :) Eric