Dear All,

Context: We are studying three plant species: A, B, and C. Our objective is to identify the ancestral species that contributed to the evolution of species C. We hypothesize that species A and B may be potential contributors.

Proposed Analysis: To test this hypothesis, we plan to conduct an ABBA-BABA analysis using the D-suite software.

Available Data:

1. Complete genome assemblies for species A, B, and C
2. All predicted coding sequences (CDS)
3. Proteomes (translated from CDS)
4. A well-annotated outgroup species (O)

Planned Steps:

1. Identify orthogroups from species A, B, C, and O using OrthoFinder Question: Should we use protein or CDS sequences for this step?

2. Concatenate multiple sequence alignments Tool suggestion: https://github.com/nylander/catfasta2phyml

Next Steps: I need guidance on how to proceed from the concatenated alignments to the D-suite analysis. Specifically:

1. What are the detailed steps to perform the D-suite analysis?
2. How do we interpret the results to answer our research question?

Your expertise and suggestions would be greatly appreciated.

Thank you,

Alexis