I have 50 species and 8 genes. My goal is to make a phylogenetic tree but the problem is that I don't have the 8 genes for all species. Some species have just one gene for example, and also most of the genes are fragmented (so for the same gene, the size is different between species).
What is the best way to do this:
1) Concatenate all genes for all species and perform a multiple alignment (so with 50 fasta)
2) Do an alignment for each genes (so with 8 fasta) and then concatenate all alignements to species level ?
3) Other methods ?
Thanks for your help.