Best tool for generating a phylogenetic tree based on gene sequences

Question

[Selenocysteine]

Hi,

I am using Seaview4 + ape in R to generate some phylogenetic trees from some genes' sequences. However, it feels like Seaview's interface is very old and also awkward to use... Someone has any suggestions? :)

Thanks

Answer 1

[Foreveremain]

There are lots - it really depends which user interface you prefer!

Seaview is widely used (and actually actively developed). I'd always recommend Jalview (www.jalview.org) if you are exploring functional and structural variation (after you've calculated a tree - we don't have phylogenetic services quite yet!). MEGA (http://www.megasoftware.net/) is very popular amongst evolutionary biologists, but I'm also biased and would recommend TOPALI if you are new to phylogenetics (http://www.topali.org/), since it is a bit more straight forward than MEGA.

For a large, but not quite-comprehensive list of software, take a look at http://en.wikipedia.org/wiki/List_of_alignment_visualization_software

[Selenocysteine]

Thank you :)