Talk:CH391L/S14/Ancestral sequence

Talk:CH391L/S14/Ancestral sequence

• --Ella Watkins (talk) 13:42, 12 February 2014 (CST) Are there programs online that can be used to apply the "Methods of inferring"? Like BLAST? If so, it might be good to add what some of those programs are. Also I know there are 2 ways of citing, but it appears to me that the more popular way is to cite according to what comes first, second etc. Maybe reconsider how you cited so that you can put number hyperlinks at the end of all of your sites.

• --Dennis Mishler (talk) 14:20, 13 February 2014 (CST) Cindy, the second figure does not display. You may need to upload the figure again.
• ----Ajv684 (talk) 18:26, 13 February 2014 (CST)This is a very comprehensive wiki, I like the way the topic was developed by starting with a brief overview and then going on explaining different approaches to obtain ancestral sequences to finally explain some concrete examples. However, I believe that presenting a comparison table to explain differences in the different approaches to derive ancestral sequences would be of great help. All those methods look very complicated to understand for a lay reader so I would as well suggest explaining the most popular one by using a figure/scheme/flow chart so that it helps making it more clear. Overall, very good wiki.

• --Liz (talk) 23:39, 13 February 2014 (CST) Lots of good information on an interesting topic here. I like the intro and history sections. Reading the Pipeline, which I think is a good way to introduce the technique, first thing is - I don't know what maximum likelihood is yet. And would it be better to say "ancestral gene sequence is inferred." You might want to add a section about the programs used to align sequences. I know it's trivial but you have a separate section for each of the other pipeline steps. Under the Methods, the limitation of Consensus Sequence should be two sentences? Why does it matter that phylogenetic relationships are ignored? You talk about the relationship between extant species used for all the methods- maybe at the top introduce why this matters. For the figure, I understand that you are illustrating the methods coming to different conclusions, but I'm not sure how you got there. What about that figure shows how you came to different conclusions based on the inference method? I really like the example of the coral. (lower wavelengths = longer wavelengths?) Did the paper give any insight into why a change in color might have helped the coral? (maybe outside the scope of this page- just wondering). Would be nice to upfront define all the classes of coral colors you name, that way when you show how it has evolved we know physically what that means. Not sure I would call the red more specific though...that means something else to me. Anyway that's definitely enough from me. Good job!