What's different between two methods of POWER?

POWER’s first method combine with MSA program to Phylip. You can just input your fasta data, then would get output of sequences alignment and phylogenetic tree.
If you already have alignment data（must be phy format）, you can use Phylogenetic anyalysis to get phylogenetic tree.

How should I setup parameters in these algorithms?

If you are not sure what different at the methods, standard parameters is your best choice. If you want to learn more about algorithms, please reference help documents.

Could I change parameters or algorithm by reconstructing phylogenetic tree?

Yes, you can change any parameters or algorithm you want.

Why do detail of POWER's output files different from my local program of ClustalW or Phylip?

First, if there are different in mismatch scores, please check again parameters are all the same with POWER and your local program.
Second, if you see some result on POWER but not on your local program, maybe some parameters about result show are different. It would not influence results.

How long can I get response?

It depends on your input sequences length and the method you choose. In average time, total sequence length small than 50000 b.p or 5000 a.a, you can get response about 5 minute.

Why would my job failed?

If you get the failed mail, please check again your parameters are all correct. If you still can’t find out the reason why job has been terminated, you can email to us include these information: your job name, email address, job send time. The information you can find on POWER’s response mail.

How many sequences would POWER tolerate?

POWER can accept 250 sequences at most. More than 3,000,00 b.p or 300,00 a.a would be ok.

Why don't I receive job mail return?

If you don’t receive job mail after one day, please resend job again and let us know.

Can I using other multiple sequence alignment data format ex.*.msa or *.aln?

Now POWER only accept PHYLIP data format ( *.phy). We are sorry for that.