tag:blogger.com,1999:blog-10781944.post8636603564340403817..comments2024-03-17T21:38:11.530-07:00Comments on The Tree of Life: New openaccess paper from my lab on "Zorro" software for automated masking of sequence alignmentsJonathan Eisenhttp://www.blogger.com/profile/07953790938128734305noreply@blogger.comBlogger7125tag:blogger.com,1999:blog-10781944.post-48896941183068297922012-02-14T19:48:59.753-08:002012-02-14T19:48:59.753-08:00Good idea. We should talk.Good idea. We should talk.Martin Wuhttps://www.blogger.com/profile/00579370840172693314noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-68978929107604078112012-02-11T13:57:29.870-08:002012-02-11T13:57:29.870-08:00Also, there is an alignment uncertainty symposium ...Also, there is an alignment uncertainty symposium at SMBE in Dublin this year. You should consider presenting Zorro, if you are not already.Reed A. Cartwrighthttps://www.blogger.com/profile/09424752191244830656noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-31122407353025370642012-02-11T13:53:32.019-08:002012-02-11T13:53:32.019-08:00Hi Martin and Jonathan,
The purpose of Zorro is t...Hi Martin and Jonathan,<br /><br />The purpose of Zorro is to mask reliable and unreliable regions of an alignment, correct? With PICS-Ord we convert the unreliable regions (post masking) into pseudo-characters that capture much of the phylogenetic information that exists in these regions. Right now we are using Viterbi-esque distance scores produced by Ngila, but I do want to use the forward-backward distance scores produced by the software I wrote for <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734402" rel="nofollow">Cartwright (2009)</a>. (The software needs to be written to be more robust, which is why I haven't distributed it yet.)<br /><br />So the way I see the two programs working together is 1) Zorro discovers regions with low alignment support and then 2) picsord converts these regions to pseudo-characters to aid reconstruction.Reed A. Cartwrighthttps://www.blogger.com/profile/09424752191244830656noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-1990944795527465582012-02-09T15:31:07.990-08:002012-02-09T15:31:07.990-08:00Hi Reed, apparently we missed your paper. Looks li...Hi Reed, apparently we missed your paper. Looks like Zorro and PICS-Ord take two complete different approaches. Not sure how to integrate them. I'm all ears if you have some ideas.Martin Wuhttps://www.blogger.com/profile/00579370840172693314noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-77780478071271063562012-02-08T23:02:02.762-08:002012-02-08T23:02:02.762-08:00OK - have gone through PICS-ORD paper and some b...OK - have gone through <a href="http://www.biomedcentral.com/1471-2105/12/10" rel="nofollow"> PICS-ORD paper </a> and some blog posts about it (from <a href="http://squamules.blogspot.com/2011/01/pics-ord.html" rel="nofollow"> Squamules </a> and <a href="http://pandasthumb.org/archives/2011/01/pics-ord-unlimi.html" rel="nofollow"> Pandas Thumb </a>. Very interesting. It would be interesting to compare and contrast how Zorro and PICS-ORD work on the same data set(s). Not sure what is going to happen with Zorro. The first author Martin is the person to discuss it with probably since he started working on it in my lab but then got one of those faculty jobs at UVA and (I assume) is going to continue to work on it if he can. I will send him a message and see if we can bring him into the conversation ...Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-49804449222237012332012-02-07T08:56:41.466-08:002012-02-07T08:56:41.466-08:00Gonna have to take a look --- was not aware of you...Gonna have to take a look --- was not aware of yours though from first skim probably should have been --- the perils of submitting a paper years ago and then just trying to finish it up and deal with reviewers comments over a few years ---Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-81323510482315483162012-02-07T08:52:03.193-08:002012-02-07T08:52:03.193-08:00Jonathan, do you have any thoughts about integrat...Jonathan, do you have any thoughts about integrating Zorro with our software, PICS-Ord?<br /><br />http://www.biomedcentral.com/1471-2105/12/10Reed A. Cartwrighthttps://www.blogger.com/profile/09424752191244830656noreply@blogger.com