Maybe error with topology of outgroup

[JJ0ONATHANESTAR]

Hello, I think I had some problem with the result of iqtree2.

Before doing iqtree, I thinned the filtered SNVs every 10000bp.
I converted this vcf file to phylip file using vcf2phylip.py.
Then I used iqtree with this command:
iqtree -s /path/iqtree/input.final.filtered.10000thin.recode.min4.phy \ -m PMB+F+R2 \ -bb 1000 \ -nt 20 \ -o Mmizolepis,Ilongicorpa \ -pre output.10000thin.1000bootstrap

I used Figtree and ete toolkit web server Phylogenetic tree (newick) viewer.
And both of them showed me result like this.

I don't know why one of the outgroup had no branch.
Even Mm is not genetically that much close to the other samples.

If you need any additional information, plz tell me. Thank you.

[bqminh]

Just to be sure: Are you really using protein model PMB? (And that this is a protein alignment). I'm not familiar with vcf2phylip, but normally VCF contains nucleotide variants.

[JJ0ONATHANESTAR]

https://github.com/edgardomortiz/vcf2phylip - this is what the vcf2phylip is.
It changes VCF into PHYLIP file, surely it contains nucleotide variants information.
And I really used PMB model. I used -m MFP option to find the best model and iqtree recommended me that.