Comments on: Phylogenetics through videoconferencing http://roberto.kellerperez.com/2009/12/phylogenetics-through-videoconferencing/ Ant reconstruction one homology at a time Tue, 29 Jun 2010 16:52:16 +0000 hourly 1 http://wordpress.org/?v=3.0 By: Roberto Keller http://roberto.kellerperez.com/2009/12/phylogenetics-through-videoconferencing/comment-page-1/#comment-1223 Roberto Keller Wed, 09 Dec 2009 15:47:36 +0000 http://roberto.kellerperez.com/?p=1882#comment-1223 <strong>Erick.</strong> Thank you for organizing these seminars. The format is a great idea. Erick. Thank you for organizing these seminars. The format is a great idea.

]]> By: Erick Matsen http://roberto.kellerperez.com/2009/12/phylogenetics-through-videoconferencing/comment-page-1/#comment-1222 Erick Matsen Wed, 09 Dec 2009 14:33:34 +0000 http://roberto.kellerperez.com/?p=1882#comment-1222 Hello Roberto-- I'm glad that you enjoyed the seminar. The recording of Ward's talk is now available. Thanks, Erick Hello Roberto–

I’m glad that you enjoyed the seminar. The recording of Ward’s talk is now available.

Thanks,

Erick

]]> By: Roberto Keller http://roberto.kellerperez.com/2009/12/phylogenetics-through-videoconferencing/comment-page-1/#comment-1221 Roberto Keller Tue, 08 Dec 2009 22:26:06 +0000 http://roberto.kellerperez.com/?p=1882#comment-1221 Regardless of the difficulties in putting direct optimization into practice, I find the whole theoretical problem related to dynamic homology fascinating. Ward Wheeler gave a talk some years ago at the AMNH about how it is possible to expand this analytical framework to incorporate process that result in changes at higher level in the molecular hierarchy from simple insertion/deletion events (gene duplications, translocations, chromosomal rearrangements, etc). It was mind-blowing. I'm also starting to see papers where people are applying direct optimization type of techniques in a Bayesian framework. Regardless of the difficulties in putting direct optimization into practice, I find the whole theoretical problem related to dynamic homology fascinating.

Ward Wheeler gave a talk some years ago at the AMNH about how it is possible to expand this analytical framework to incorporate process that result in changes at higher level in the molecular hierarchy from simple insertion/deletion events (gene duplications, translocations, chromosomal rearrangements, etc). It was mind-blowing.

I’m also starting to see papers where people are applying direct optimization type of techniques in a Bayesian framework.

]]> By: Alex http://roberto.kellerperez.com/2009/12/phylogenetics-through-videoconferencing/comment-page-1/#comment-1217 Alex Tue, 08 Dec 2009 17:51:32 +0000 http://roberto.kellerperez.com/?p=1882#comment-1217 When possible, I avoid the alignment issue altogether by sticking to protein-coding genes. Although these genes are trickier to amplify, I prefer that lab-bench level of difficulty to the downstream philosophical and modeling troubles that plague the ribosomal genes. When possible, I avoid the alignment issue altogether by sticking to protein-coding genes. Although these genes are trickier to amplify, I prefer that lab-bench level of difficulty to the downstream philosophical and modeling troubles that plague the ribosomal genes.

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