total identical sequences clustered into one orthogroup, but the topology of gene tree divided into multiple clades

[liping-jiang]

hello,

I recently worked on pan genome analysis using orthofinder2 and I found one problem: some total identical sequences clustered into one orthogroup, and gene tree built using iqtree with default parameters. I view the topology of the gene tree with ITOL, the sequences divided into three clades. But when I implemented the phylogenetic analysis using fasttree, these sequences clustered into one clade.

So I want to know which step went wrong.

I look forward to hear from you.

Best wishes

Liping

[davidemms]

Hi

It sounds like this is a question for iqtree perhaps? Can you reproduce this issue with fasttree and iqtree directly, outside of orthofinder, with the MSA files from orthofinder as input?

Another potential but unlikely case is that the sequences are actually placed in the same clade but this is obscured by the root chosen for the tree. You could check if the tree can be re-rooted anywhere such that all the genes are in a single clade.

All the best David