General musings from the MacVector team about sequence analysis, molecular biology, the Mac in general and of course your favorite sequence analysis app for the Mac!

Clustering an alignment

Sometimes it is useful to sort, or cluster, an alignment according to the similarity/identity of its sequences. With such a sorted alignment you are able to more easily visualise closely related sequences as they will be together in an alignment with more distantly related sequences being much further apart.

If you want to quickly cluster a sequence alignment in MacVector then you can use a phylogenetic tree to do this.

– Take your sequence alignment and run a phylogenetic reconstruction. In the MSA editor click the TREE button or run the menu command:

ANALYZE > CONSTRUCT TREE

– From the resulting phylogenetic window, you can rearrange sequences if necessary by selecting nodes and “rotating” them with the toolbar buttons.

– Then, with the focus on the Phylogeny window, sort the alignment to match the tree using the Sort MSA toolbar button or using the menu command:

ANALYZE > PHYLOGENETIC ANALYSES > SORT MSA TO MATCH TREE

This will rearrange the sequences in the editor to match the phylogeny branches.

MSA_Tree.png

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