Construct and Refine a Multiple Sequence Alignment

1. Download sequence test-set gp120.fasta
   http://www.tbi.univie.ac.at/~xtof/Leere/300632/Data/gp120.fasta
2. Align protein sequences using MultiAlign. (Use default parameters).
   http://bioinfo.genotoul.fr/multalin/
3. Validate multiple sequence alignment using Rascal from PipeAlign.
   http://bips.u-strasbg.fr/PipeAlign/
4. Eliminate poorly aligned / divergent positions from the alignment using GBlocks.
   http://molevol.cmima.csic.es/castresana/Gblocks_server.html
5. Use Readseq to convert multiple sequence alignment to PHYLIP|PHYLIP4 format.
   http://iubio.bio.indiana.edu/cgi-bin/readseq.cgi