alignment with phylogenetic tree

Question

[qwzhang0601]

I have phylogenetic tree of 100 species, and I also have the multiple sequence alignment file for a gene we are interested in. I wonder whether there is some tool to generate a plot which shows both phylogenetic tree of the 100 species and sequence alignment of the gene from 100 species?

Thanks

Answer 1

[Mensur Dlakic]

MEGA does both things you want, though it is not my tool of choice for either task. Is there a reason you need to use a single program for both tasks?

Answer 2

[qwzhang0601]

Thank you! Briefly, I want to show multiple sequencing alignment. Some sites under positive selection may evolve differently among different species. So I want to order the sequences according to the phylogenetic tree of those species. Thanks