I have lots of sequences to align and I used to use MEGA6 but it takes forever to finish one multiple alignment session. I need a faster and a more accurate way of obtaining my multiple alignments.
Trying using MEGA6 on a Computer with higher configuration (Faster speed).
MAFFT is good but try using CLC main workbench for MSA..Its worth trying.
Trying using MEGA6 on a Computer with higher configuration (Faster speed).
you can also try the Muscle:
http://www.ebi.ac.uk/Tools/msa/muscle/
(There is currently a limit of 500 sequences and 1MB of data).
while using large data-sets there is always a problem of system memory, i would say try a better PC with large enough RAM and then run mega 6, i would prefer muscle over clustal option which takes long time to run sometimes overnight and might hang your pc. i agree with filipe above in ebi's muscle version having a problem of file size. very recently i have tried up-to 400 sequences executing muscle in mega 6.0. i sometimes align sequences online at the ebi or some Japanese server for clustalw. then perform phylogenetic analysis on my own PC by downloading the fasta format alignments. best of luck.
If you are looking for a purely online program I prefer ClustalW over MAFFT. I find that my alignments are a little better as it gives me the option to input a few more parameters. That being said, there are much better programs out there if you have the CPU to handle as Jainder Chhillar suggested.
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