9.4 Alignment masking

To mask or strip columns from your alignment, go to Tools Mask Alignment. This tool can be used to add “Masked” annotations to sites or to create a copy of your alignment with some sites removed. Sites can be removed or masked by sequence content (e.g., you can remove all gaps, or all constant sites), codon position, existing Masked annotations, or using a NEXUS-style CHARSET. For the purposes of phylogenetic analyses, you can use this tool to create alignments from which any sites with Masked-type annotations will be removed (see section 12.2.1 ).

    Masking sites by sequence content:
    Mask sites by codon position:
    Remove masked sites:
    Mask sites defined by a NEXUS-style CHARSET:
Masking sites by sequence content:

Sites can be masked or stripped based on the following sequence content:

When deciding whether or not to remove a site, regions annotated as Trimmed will not be considered.

Mask sites by codon position:

1st, 2nd and/or 3rd codon positions can be masked or stripped by checking the codon positions that you do not want to analyze. Note that this option always takes the first base in your alignment to be codon position one, regardless of any ORF or CDS annotations that may be on your sequences. Available for nucleotide sequences only.

Remove masked sites:

If you already have an annotation track on your sequence containing Masked annotations, then you can strip these regions by choosing the “masked sites” option and the track you wish to use. Only masks applied to the consensus sequence of an alignment are used for stripping.

Mask sites defined by a NEXUS-style CHARSET:

Sites can be masked or stripped based on a NEXUS-style CHARSET entered into the text area. This must conform to the NEXUS CHARSET specifications (see Maddison, Swofford & Maddison 1997). Both standard or vector style CHARSETs can be used.

For example, both of the following would mask or strip sites 2, 4, 5, and 6 from an alignment with 10 sites.

Standard style: 2 4-6; Vector style: 0101110000