Multiple Sequence Alignment

From MultiSeq, export sequences in FASTA format (File ‣ Export: All Sequences, Sequence Data (FASTA), Include sources in FASTA header).

Create a multiple sequence alignment(MSA) with MAFFT (or ClustaLW or tCOFFE or Muscle). Here we use the MAFFT server:

Upload to the MAFFT server (use defaults).

  • download alignment (ALN and FASTA) (Save link as adk_msa_mafft.aln (Clustal MSA format) and adk_msa_mafft.fasta (FASTA))
  • visualize the phylogenetic tree
  • visualize the alignment (see also Jalview)

Then use your saved alignment to create a WebLogo (check Multiline Logo). Download as PDF or PNG.