For heterozygosity

[rayanans]

Hello,

Any one know if we can use bases such as W, R, Y, etc. for heterozygous sequences. Also, how it effects in alignment and build tree?

[Peter Richterich]

Can I use bases such as W, R, Y, etc. for heterozygous sequences?

Yes. There are also several functions in CodonCode Aligner that you may find useful. The first one is to automatically edit double peaks in chromatograms to ambiguities. This is available through the "Edit" menu by selecting "Change Bases" => "Call Second Peaks". For more information, please check the online help ("Help" menu => "Aligner Help").
The second feature that might be useful is mutation analysis. For more information, please visit http://www.codoncode.com/aligner/quicktour/snps.htm.

Also, how it effects in alignment and build tree?

In alignments with CodonCode Aligner's built-in algorithms, ambiguities are counted as matches when appropriate (e.g. an alignment of "W" to an "A" or "T"), and as mismatches otherwise (e.g. "S" and "A"). When using external tools (Clustal, Muscle, Bowtie2), this may be different; please check the documentation for these programs.
When building trees, simple possible matches (like W and A or T) will counted as matches. Alignments where some positions have different ambiguities may produce non-intuitive results.

[rayanans]

Many thanks Peter for helpful information.