I have assembled the mitochondrial genome of 8 sheep individuals and now I am trying to construct the phylogenetic tree.
I have also downloaded from ncbi 2 representatives from each haplogroup. (So, I have 18 mitochondrial genomes in total).
With clustal omega I did the multiple alignments online and I used RAxML for the generation of 500 ML trees.
I did bootstrapping (number of bootstrap replicates: 2000) but I'm not so confident with the bootstrap values.
Well, the topology seems ok, since all my samples belongs to haplogroup B and that is obvious from the tree, but the bootstrap values between them are low. 50, 48, even lower.
The bootstrap numbers at the major branches (the branches that categorizes the haplogroups) are very good (100, 98, etc). The problem seems to be in the small branches among my individuals.
I try to build a tree only with my individuals but again, I have some very good values (around 100) but also and some weak.
As it seems, I'm doing something wrong in my methodology but I cannot think what is.
Could you help me with the steps that I have to follow?
Thank you very much in advance,