For phylogenomic analysis of closely related species, it is important to work with long, non-recombining regions. Ideally one could also work with regions where the mutational dynamics are well understood. Thus genes are ideal. However, while many studies may use CDS of genes for this, merged CDS could be quite some distance apart. Ideally, being able to select single exon per gene, > min_length and < max_length, would allow one to work with exons genome wide that pass thresholds.
In sum, the ability to quickly and robustly pull exons per gene, would aide in phylogenomic analyses, as these could serve as the input for gene tree reconstruction, which could then be used in ASTRAL analyses. Using a single exon per gene adheres to a multi-species coalescent framework.
For phylogenomic analysis of closely related species, it is important to work with long, non-recombining regions. Ideally one could also work with regions where the mutational dynamics are well understood. Thus genes are ideal. However, while many studies may use CDS of genes for this, merged CDS could be quite some distance apart. Ideally, being able to select single exon per gene, > min_length and < max_length, would allow one to work with exons genome wide that pass thresholds.
In sum, the ability to quickly and robustly pull exons per gene, would aide in phylogenomic analyses, as these could serve as the input for gene tree reconstruction, which could then be used in ASTRAL analyses. Using a single exon per gene adheres to a multi-species coalescent framework.