I am working on a few snake genera. In my 16S multiple sequence alignment I get gaps with ambiguously aligned region in alignment matrices, which happens to be part of 16S loop structure. It seems that the gaps tend to be species specific and unique characteristics of a species. I have a potential new species in my data with unique gaps and number of nucleotide base characteristics. Now I would like to know how to treat these ambiguously aligned region or gaps? Whether I exclude it from analysis or treat it as characters? Please suggest!
Hi. first of all i doubt that you have 16S sequences of snakes.. It is 18S. And gaps are not included in the calculation of phylogenetic trees. You have to exclude these gaps also in all the other sequences..
Thanks for suggestion! So far I am excluding those ambiguously aligned region/gaps in my analysis. It is 16S.
Hello Ashok.
Phylogenetic methods can not deal with gaps, so get rid of them. Do no forget them though. Gaps exist, and probably they will make sense once the tree is done. As you said, they might be species specific, so gaps would give you a sentence in the "discussion-part-of-the-paper" supporting the phylogenetic tree.
Hi Ashok,
it is true that gaps are automatically excluded from alignments in most tree building algorithms. However, they can be highly informative in terms of presence/absence and lenght within the alignment (especially valuable for species delimitation!). In fact, there is a very easy-to-use software called GapCoder which uses simple indel coding to generate a 0/1 matrix. You can append this matrix to your alignment, and, e.g., include it as a second partition in MrBayes. Feel free to contact me if you have further questions.
cheers,
-tom
- Badges
- Science topic
- Similar topics
- Geoscience
- Atmospheric Sciences
- Climate Science
- Climate Change