Question: Infer ancestral sequence from a Multiple Sequence Alignment
gravatar for anuragm
6.0 years ago by
anuragm130 wrote:

I am trying to infer the ancestral state from a MSA that I have using MEGA. However, I am not sure how I will get a sequence as the ancestral state when there is no input in form of a MSA into the ancestral state reconstruction feature in MEGA. I am also not very sure how to interpret the output that comes in form of an excel sheet. I could not find a MEGA tutorial online for this. Could someone please point me towards online resources that could help me ?

ADD COMMENTlink modified 6 months ago by Biostar ♦♦ 20 • written 6.0 years ago by anuragm130

See here for options: Is FastML a good server for reconstructing ancestral protein sequence?

ADD REPLYlink written 6.0 years ago by Michael Dondrup48k

FastML crashed multiple times, just like it is mentioned!

ADD REPLYlink written 6.0 years ago by anuragm130

Although this was posted a while ago, I thought I might offer a suggestion for anyone who stumbles across this in future - As far as I am aware, FastML can only handle less than 300 sequences (maybe even less than 200). So if you have more than this amount, try reducing the number. 

ADD REPLYlink written 5.9 years ago by JulianZ70
gravatar for Biojl
5.9 years ago by
Biojl1.7k wrote:

The easiest way to do it is to use the PRANK multiple alignment. Is as easy as activating the -showanc option when calling the command to build the MSA.

Notice that PRANK requires a phylogenetic tree as input, although it can also calculate it automatically using mafft (read the manual).

ADD COMMENTlink written 5.9 years ago by Biojl1.7k
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