Question: Best tool for generating a phylogenetic tree based on gene sequences
0
gravatar for Selenocysteine
5.5 years ago by
Dublin, Ireland
Selenocysteine600 wrote:

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.

ADD COMMENTlink modified 4.1 years ago by Biostar ♦♦ 20 • written 5.5 years ago by Selenocysteine600
3
gravatar for Foreveremain
5.5 years ago by
Foreveremain60
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 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

 

ADD COMMENTlink written 5.5 years ago by Foreveremain60

Thank you :)
 

ADD REPLYlink written 5.5 years ago by Selenocysteine600
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