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Sequence Alignments

  • MUSCLE. Multiple Sequence Alignment. Also has a nice web interface to submit jobs directly online
  • MAFFT. Multiple Sequence Alignment program for unix-like operating systems. Alternative to MUSCLE
  • t-coffee. Multiple Sequence Alignment. Alternative to MUSCLE
  • clustalW2. Multiple Sequence Alignment. Alternative to MUSCLE
  • MEGA. integrated tool for conducting sequence alignment, inferring phylogenetic trees, estimating divergence time. Fantastic GUI.
  • BioEdit Sequence Alignment Editor (for PC only) with various molecular evolution functions. Nice GUI. Use to be one of the leading program. Outdated?
  • Most proprietary software (Sequencher, Geneious, CLC Genomics) will also permit multiple sequence alignments.