Alignments are statements of homology: we assume that amino acids or nucleotides at the same position have evolved from the same ancestral residue. In practice, however, it is often difficult to have any confidence in this homology for some regions of the alignment, and these should be omitted from the phylogenetic analysis. MacVector allows you to mask any positions in the alignment, to exclude them from the analysis. This is done in the MSA Editor window. When you enable the position masking tool, a blue bar appears above the alignment. By clicking in this bar at the appropriate locations, you can mask particular sites, which appear grayed.
TIP: If you save the multiple alignment as a NEXUS file, the position mask will be saved with it (as an exclusion set in the assumptions block of the file).
By default, position masking is not enabled, and there is no blue bar displayed above the alignment in the MSA editor window.
1. With the multiple alignment in an active MSA editor window, select the preferences button on the toolbar.
The Multiple Alignment Options dialog box is displayed.
2. Select the Editor tab, and select the Show Position Mask check box to enable it. Then select OK.
The blue position masking bar is displayed above the alignment in the MSA Editor window.
3. Select the positions to mask, using the mouse as follows: