For heterozygosity

Find answers to common questions for CodonCode Aligner and the Aligner License Server

For heterozygosity

Postby rayanans » Wed Jan 21, 2015 1:08 pm

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?
rayanans
 
Posts: 2
Joined: Wed Jan 21, 2015 7:12 am

Re: For heterozygosity

Postby Peter Richterich » Wed Jan 21, 2015 1:56 pm

rayanans wrote: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.

rayanans wrote: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.
Peter Richterich
Site Admin
 
Posts: 100
Joined: Thu Aug 21, 2008 7:23 pm

Re: For heterozygosity

Postby rayanans » Wed Jan 21, 2015 3:03 pm

Many thanks Peter for helpful information.
rayanans
 
Posts: 2
Joined: Wed Jan 21, 2015 7:12 am


Return to Support & Questions



Who is online

Users browsing this forum: No registered users and 96 guests