Beginner's Question: Rooting Phylogenies to proceed with IQ2MC workflow

[walkyshitake]

Hello,

I am running IQTREE v3.0.1 Windows with proteins sequences from a gene family of interest. My command line was:
iqtree3.exe -s seq.fasta.

My goal is to construct an ultrametric tree based on the maximum likelihood tree output from IQTREE and estimate the divergence time using MCMCtree.
I am aware that the command I mentioned will only construct an unrooted tree, which I need to check on root phylogenies directory for a next-step guidance. I am uncertain how to obtain a NEXUS partition file. Should I use the command:
iqtree3 -p FOLDER_NAME --out-aln OUTFILE_NAME
to generate it?

I would greatly appreciate any guidance or clarification on this matter. Thank you for your time and assistance.

[crispimcatfish]

Hi,
I hope this finds you well.
How are your analyses and studies going? All ok?
I'm working with UCE data and using the AMAS software to generate my concatenated matrix and partition file (you can adjust it to your data):
AMAS.py concat
-i *.fasta
-f fasta
-d dna
-u phylip
-t supermatrix.phy
-p partitions.nex
--part-format nexus

And for generate tree, I'm also using IQTree v.3:
iqtree -s supermatrix.phy -p partitions.nex -m GTR+G -bb 1000 -nt 20 -pre arvore_final

To root, using ape, on R:
library(ape)
tree <- read.tree("arvore_final.treefile")
tree_rooted <- root(tree, outgroup="outgroup_sequence_x", resolve.root=TRUE)
write.tree(tree_rooted, "tree_rooted.tre")

Some adjustments may be provided to you personal dataset.
I hope this answer help you.
Best, Jeff

[bqminh]

@piyumalanthony can you help?

[piyumalanthony]

Hi @walkyshitake,

You can use iqtree3 -p FOLDER_NAME_FOR_PARTITION_DATA --out-aln OUTFILE_NAME to generate a partition nexus file, and then IQ-TREE can be executed with the above-generated partition nexus file and concatenated alignment.

To root the unrooted tree from IQ-TREE, you can use Figtree or the R code above provided.
You need to run IQ-TREE again for dating with --dating mcmctree flag and the rooted tree. This will generate the necessary files for the mcmctree specific to the rooted tree. Hope this answers your question.