I have created a phylogenetic tree (with 500 bootstrap iteration) based on
AMPHORA enter link description here tool specified marker genes (28 marker protein sequences were extracted from 30 bacterial genome and concatenated, aligned by
mafft and trimmed by
gblock server). Even though the alignment is so good, but half of the clades bootstrap value is 10 to 20. I tried with various models, despite I could not get good bootstrap values (
70 above). Is it possible to improve the bootstrap value in any way?
Thank you in advance.