I have a question regarding building phylogenetic trees. I am working with pooled (n = ~ 500) PACBio sequencing material with reads of ~ 4kb length. I am not very familiar with the current methods for building trees, so was wondering whether someone could help me out! I tried clustalw2 to draw an 'instant' tree and is really fast, but does not show very good results so far. I also tried RAxML by converting a vcf to a phylip, but I believe this does not take indels that well into account.
Thank you so much in advance, Annabel