Question: Best tool for generating a phylogenetic tree based on gene sequences
gravatar for Selenocysteine
5.5 years ago by
Dublin, Ireland
Selenocysteine600 wrote:


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? :)


ADD COMMENTlink modified 4.1 years ago by Biostar ♦♦ 20 • written 5.5 years ago by Selenocysteine600
gravatar for Foreveremain
5.5 years ago by
United Kingdom
Foreveremain60 wrote:

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

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

For a large, but not quite-comprehensive list of software, take a look at


ADD COMMENTlink written 5.5 years ago by Foreveremain60

Thank you :)

ADD REPLYlink written 5.5 years ago by Selenocysteine600
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