I would try Clustal Omega (http://www.ebi.ac.uk/Tools/msa/clustalo/)!

I haven't tried MAFFT, but MUSCLE is much better than Clustal.

you can try MUSCLE, Clustal , Multalign and offline softwares like MEGA (which run both Clustal and MUSCLE)

MUSCLE, esp. thanks to convenience of running it through a command-line interface, very efficient if one needs to use unattended batch mode for very many input files

In addition to these, you may try CLC genomics workbench 6.0, It gives better multiple sequence alignment and also identifies the percentage conservedness amongst your sequences as well as the conserved domainns.

MUSCLE and MAFFT are two of the best

It's depends what kind of sequences you want compare if it is from close related organism try Clustal Omega, for distance organisms try Muscle.

Hi, I am working with MAFFT but maybe this overview is interesting?! http://en.wikipedia.org/wiki/List_of_sequence_alignment_software

Cheers, Nadine

clustalW and Bio-edit are best for Alignment so you can go for it