I have more than 4000 files containing orthologous gene clusters in each file from a bacterial community. How can I perform multiple sequence alignment of all the files in fast and efficient manner? Should I use clustal W, if yes how?
If you need really fast alignment, I suggest you to try mafft (http://mafft.cbrc.jp/alignment/software/), it has some really fast and accurate methods for that. But if your files are small you can use clustalw / clustal omega / muscle / t_coffee or whatever you want.