From stevet from bio.fsu.edu Mon Nov 3 15:56:23 2008 From: stevet from bio.fsu.edu (Steve Thompson) Date: Tue Nov 4 05:27:31 2008 Subject: [Molecular-evolution] Other: Re - GCG non-support In-Reply-To: <46B83135.7050107@ebi.ac.uk> References: <46B1AEA8.2040308@ebi.ac.uk><20070802081845.D3246@epsilon.bio.fsu.edu><46B2F2E3.4020305@ebi.ac.uk><20070803131050.H7747@epsilon.bio.fsu.edu><1186251135.996351.149470@g12g2000prg.googlegroups.com> <46B721F0.8050407@ebi.ac.uk> <7930EE6CD7CA354D93B444D0433C061103A8C70D@NIHCESMLBX6.nih.gov> <46B83135.7050107@ebi.ac.uk> Message-ID: <20081103121427.E74728@epsilon.bio.fsu.edu> Hi Peter - I'm picking back up on an old thread from summer 2007 re. the Acclerys GCG 'retirement.' Since that time several developments, only a few positive in my opinion, have clarified the situation. One - my online petition at www.petitiononline.com was very successful (http://bio.fsu.edu/~stevet/Accelrys_petition.pdf) in gathering signatures, almost 200 in a month, and in fostering international exposure, as the BioInform article from April 2008 attests (http://bio.fsu.edu/~stevet/BioInformGCG.pdf). But Accelrys remains committed to not releasing any GCG code, due to exhorbiant and without profit legal expense. So be it and understood - we tried. Two - Accelryrs did distirbute the 'perpetual' licenses to all valid license holders that were entitled to it, as I announced in this forum April 2008, and they worked great, even across multiple nodes in a cluster. Thany you Accelrys. However . . . Three - We (FSU) upgraded our Linux cluster that supports GCG and many other bioinformatics tools to CentOS version 5. Unfortunately, almost half of the GCG package now fails due to unresolvable library conflicts (as I warned would happen - unfortunately sooner than I had hoped). Our systems operations folk initially thought they could fix this but the solution has remained ellusive. The affected programs are all the oldest 'legacy' programs in the package, although some longtime GCG pragrams like Pearson's FastA package remain viable. Four - SeqLab continues to operate just fine, but without access to many of the analytic tools of the package, its usefullness is quite impacted, though I still think it's one of the best multiple sequence alignment editors around. This is where you come back in Peter. It may seem odd to ask, but the need is actually larger now that so much of the package no longer works in an Enterprise (or CentOS) Linux version 5 environment. I'm sure that I am not alone in this situation. So here goes - I've asked it many time before, and I've begun to do the work myself starting with PlotCon, but has anybody built SeqLab extension configuration files to launch EMBOSS programs? Cheers - Steve Steven M. Thompson A C T G stevet@bio.fsu.edu \-/ http://bio.fsu.edu/~stevet/cv.html /\ /--| FSU SCS / BioInfo 4U /---/ |--/ Florida State University School of \-/ Computational Science /\ /--\ 1st floor DIRAC 150G |---\ Tallahassee, Florida \---\ 32306-4120 \--| 850-644-4490 \-/ /\ 2538 Winnwood Circle /--\ Valdosta, Georgia /---| 31601-7953 |--/ 229-249-9751 From gidey1998ec from yahoo.com Sun Nov 16 11:48:39 2008 From: gidey1998ec from yahoo.com (Gidey Yirga) Date: Mon Nov 17 10:29:56 2008 Subject: [Molecular-evolution] asking phd studentship Message-ID: <761113.43416.qm@web56504.mail.re3.yahoo.com> Dear Sir/ Madam I am an Ethiopian citizen currently working in higher institution called Mekella University as lecturer. I would like to enquire PHD scholarship grant. My proposal is Peri-urban biodiversity management: wildlife around Mekelle University, with a focus on the top predator spotted hyena. Would you pleas help me in getting this opportunity. Thanks in advance for your email. Best wishes for you ??? Yours Gidey Yirga -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/mol-evol/attachments/20081116/bc8e6167/attachment.html From areitzel from whoi.edu Tue Nov 18 09:31:28 2008 From: areitzel from whoi.edu (areitzel@whoi.edu) Date: Tue Nov 18 09:57:34 2008 Subject: [Molecular-evolution] Comparing distances for two trees Message-ID: <1227018688.4922d1c0341d0@webmail.whoi.edu> I am interested in comparing phylogenetic distances between two trees. The two trees are likelihood trees for different proteins, but each tree has the same taxa to facilitate pairwise comparisons. I was hoping someone could give me some advice on how to compare these two distance matrices. The trees do not have the same topology so the order of the taxa varies between the distance matrices for the two proteins. The goal for this project is to test for co-evolution of the two proteins via regression. Thanks in advance for any assistance. ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From ppuigbo from gmail.com Tue Nov 18 11:52:09 2008 From: ppuigbo from gmail.com (ppuigbo@gmail.com) Date: Sat Nov 22 13:49:55 2008 Subject: [Molecular-evolution] Comparing distances for two trees In-Reply-To: <1227018688.4922d1c0341d0@webmail.whoi.edu> References: <1227018688.4922d1c0341d0@webmail.whoi.edu> Message-ID: Last year, we published(*) a new software to compare phylogenetic trees that may be useful for your project. The program is called TOPD/FMTS and it's freely available at http://genomes.urv.cat/topd . (*) Puigbo P, Garcia-Vallve S, McInerney JO. Bioinformatics, 2007. 23:1556-1558. 2008/11/18 > I am interested in comparing phylogenetic distances between two trees. The > two > trees are likelihood trees for different proteins, but each tree has the > same > taxa to facilitate pairwise comparisons. I was hoping someone could give > me > some advice on how to compare these two distance matrices. The trees do > not > have the same topology so the order of the taxa varies between the distance > matrices for the two proteins. The goal for this project is to test for > co-evolution of the two proteins via regression. Thanks in advance for any > assistance. > > > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > _______________________________________________ > Mol-evol mailing list > Mol-evol@net.bio.net > http://www.bio.net/biomail/listinfo/mol-evol > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/mol-evol/attachments/20081118/50c80d37/attachment.html