Comments on: Improving Multiple Sequence Alignments with a Phylogeny-Aware Algorithm http://anthropology.net/2008/06/20/improving-multiple-sequence-alignments-with-a-phylogeny-aware-algorithm/ Beyond bones & stones Sat, 21 Nov 2009 23:33:20 +0000 http://wordpress.com/ hourly 1 By: Chris http://anthropology.net/2008/06/20/improving-multiple-sequence-alignments-with-a-phylogeny-aware-algorithm/#comment-13510 Chris Fri, 23 Jan 2009 15:50:45 +0000 http://anthropologynet.wordpress.com/?p=926#comment-13510 Actually, in this study, they did not compare sequences of primates to primates, primates to rodents, and primates to all mammals. Rather, they simulated synthetic DNA sequence data. "Fo the 16-taxon tree, we set evolutionary relationships close, intermediate, and distant, approximately representing comparisons of primates, primates and rodents, and mammals, respectively." This is a difference. I think one cannot learn something about the frequency of indels from this study, because the frequency of indels actually went into their model as a parameter and was not a result. They were not able to "identify that insertions are far more common in primate evolution than deletions" -- this is an assumption they made! Actually, in this study, they did not compare sequences of primates to primates, primates to rodents, and primates to all mammals. Rather, they simulated synthetic DNA sequence data.

“Fo the 16-taxon tree, we set evolutionary relationships close, intermediate, and distant, approximately representing comparisons of primates, primates and rodents, and mammals, respectively.”

This is a difference. I think one cannot learn something about the frequency of indels from this study, because the frequency of indels actually went into their model as a parameter and was not a result.

They were not able to “identify that insertions are far more common in primate evolution than deletions” — this is an assumption they made!

]]> By: Sphaerula » More Accurate Multiple Sequence Alignment http://anthropology.net/2008/06/20/improving-multiple-sequence-alignments-with-a-phylogeny-aware-algorithm/#comment-11524 Sphaerula » More Accurate Multiple Sequence Alignment Sun, 29 Jun 2008 18:01:39 +0000 http://anthropologynet.wordpress.com/?p=926#comment-11524 [...] anthropology.net [...] [...] anthropology.net [...]

]]>