Can you do a sequence alignment with an uneven number of genes? (For phylogenetics)

Question

[YOUSEUFS]

Not all of my organisms in question contain all the genes I want to use for sequence alignment, can I keep them in anyway and do the alignment to create a tree?

[GenoMax]

You could create gene specific trees in that case.

Answer 1

[h.mon]

You can, but it is probably best to remove sparse genes (genes missing from a high percentage of taxa, say 50%, or 80%). Also, probably good to remove taxa with a high proportion of missing genes. I am not up to date with the latest literature, though, so I don't know the most accepted thresholds.

Alternatively, you can reconstruct trees on a gene by gene basis, then use some tree conciliation / supertree method to obtain the final tree.