Multiple Sequence Alignment Programs

You have access to two multiple sequence alignment programs in your lists: MAFFT and ClustalW. You can apply it to your lists. Note: If you have a list with many contigs, these programs may take along time to finish.

After you have selected a list, you will see the "Analyze list" dropdown menu.

MAFFT:  Multiple Sequence Alignment Program.

MAFFT: Multiple Sequence Alignment Program.

MAFFT

MAFFT is a multiple alignment program for amino acid or nucleotide sequences. After you have selected MAFFT, you will be presented with the following dialogue box:

MAFFT Dialogue Box.

MAFFT Dialogue Box.

You can select Sequence type and check additional options. Click on Run MAFFT to start the program. The results provide you with the alignment sequences, a circular dendrogram, and a tree diagram.

MAFFT: Alignment sequences.

MAFFT: Alignment sequences.

MAFFT: Circular dendrogram.

MAFFT: Circular dendrogram.

MAFFT: Tree diagram.

MAFFT: Tree diagram.

You can use the links provided to download the protein sequences in .aln and .fasta formats, as well as the visualizations.

Clustalw

Similarly, ClustalW is a general purpose DNA or protein multiple sequence alignment program. After you have selected ClustalW, you will be presented with the following dialogue box:

Clustalw: Dialogue box.

Clustalw: Dialogue box.

And you also get the results in alignment sequences, circular dendrogram, and tree, along with all the download links.

Clustalw: Alignment sequences.

Clustalw: Alignment sequences.

Clustalw: Circular dendrogram.

Clustalw: Circular dendrogram.

Clustalw: Tree diagram.

Clustalw: Tree diagram.