I need to reconstruct ancestral sequences in evolution of short peptides. Trying all possible models in FastML I obtained results that just didn't make much sense. In Mesquite there are currently no available likelihood models for protein evolution...
For me this is a first experience in this field. You, who do have some experience with peptide (or more likely protein) evolution reconstructions, which programmme would you recommend to use?
Thanks
Dear Zuzana, I recommend you to try MEGA which works well for reconstructing the ancestral state of a specific peptide sequence. For details you can have a look here:
Rapid evolution of antimicrobial peptide genes in an insect host–social
parasite system (doi: 10.1016/j.meegid.2014.02.002)
Good luck, Silvio
Hi Zuzana,
As previously mentioned, MEGA should do the job, I used it also for that purpose on short proteins (65 aa).
But I just want to add a general comment here. You must be sure to have a "good" dataset to begin with.
Your sequences must not be too divergent (with few Indel), either the reconstruction MEGA will give you (cos it will every time end up with something) will not make more sense. The "robustness" of the reconstruction and your confidence in it also depends on your research goal...
Best wishes,
Guillaume
Did you try RaxML? It's a phylogeny reconstruction software mostly used for generating trees, but it also has an ancestral reconstruction feature.
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