=== Sequence Alignments ===

  *[[http://www.ebi.ac.uk/Tools/msa/muscle/|MUSCLE]]. Multiple Sequence Alignment. Also has a nice web interface to submit jobs directly online
  *[[http://mafft.cbrc.jp/alignment/software/|MAFFT]]. Multiple Sequence Alignment program for unix-like operating systems. Alternative to MUSCLE
  *[[http://www.tcoffee.org/Projects/tcoffee/|t-coffee]]. Multiple Sequence Alignment. Alternative to MUSCLE
  *[[http://www.ebi.ac.uk/Tools/msa/clustalw2/|clustalW2]]. Multiple Sequence Alignment. Alternative to MUSCLE
  *[[http://www.megasoftware.net/|MEGA]]. integrated tool for conducting sequence alignment, inferring phylogenetic trees, estimating divergence time. Fantastic GUI.
  *[[http://www.mbio.ncsu.edu/bioedit/bioedit.html|BioEdit]] Sequence Alignment Editor (for PC only) with various molecular evolution functions. Nice GUI. Use to be one of the leading program. Outdated (?) and no longer supported.
  *Most proprietary software (Sequencher, Geneious, CLC Genomics) will also permit multiple sequence alignments.