Did you try MUSCLE (http://www.drive5.com/muscle/)?
You can use it at http://www.ebi.ac.uk/Tools/msa/muscle/, but such a big query might be stopped.
Mauve should be pretty quick and shouldn't need much resources, just go ahead and try it.
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aligning whole chloroplast genomes
I have over 40 whole chloroplast genomes to align for purposes of eventually doing a phylogenetic analysis. They are from very closely related individuals (e.g. within species).
I have been running MAFFT via the Guidance server for about a month now. I am guessing this isn't going to work. My question is, how long can I expect this to take using MAFFT straight up (the online server or the download version) or Mauve? What sort of computational power is needed (can I use these programs on a desktop)? Finally, are there other suggestions for generating a multiple sequence alignment of this many sequences with this many residues (~150,000 bp)?
Any help is greatly appreciated (still a novice here!).
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