Hi all. I'm rather surprised that Jalview has yet to be mentioned: http://www.jalview.org/
Although I've heard that ESPript can make the best looking figures, Jalview is also capable of generating very beautiful output, and I've found it reasonably intuitive and plenty powerful. I'm not fond of the command line, so the Jalview GUI is especially sweet for me. -Joel On Wed, May 26, 2010 at 2:13 AM, Sebastiano Pasqualato < sebastiano.pasqual...@ifom-ieo-campus.it> wrote: > > Thanks Roger, > that worked perfectly! > I'll try and have fun with aline now. > ciao, > s > > On May 25, 2010, at 7:56 PM, Roger Dodd wrote: > > Hi there, > > I just got this working a couple of days ago under Mac OS X 10.6.3. I > manually compiled and installed Perl-Tk from CPAN. Steps taken: > > 1. Download and ungzip / untar: > http://search.cpan.org/CPAN/authors/id/S/SR/SREZIC/Tk-804.028_501.tar.gz(the > newer -503 version didn't work) > 2. Change into the directory > 3. Execute perl Makefile.PL > 4. make > 5. make test > 6. sudo make install > > Hopefully that should get things working. > > Cheers, > > Roger > > On 25 May 2010 17:50, Sebastiano Pasqualato < > sebastiano.pasqual...@ifom-ieo-campus.it> wrote: > >> Hi there, >> I remember a friend of mine showing me Aline, and it looked very nice. >> However, I can't make it work on my MacBook Pro (Mac OS X 10.6.3). >> With respect to the instruction I found on the website, I had to change >> the export lines to be added to the .bashrc in order not to get error >> messages. >> That's how I added the path info: >> >> export ALINEHOME='/sw64/share/xtal/aline_011208' >> export PATH=$PATH:$ALINEHOME/bin >> >> however, I still get an error while trying to run aline: >> >> s...@host005:~> aline >> Can't locate Tk.pm in @INC (@INC contains: /sw64/lib/perl5 >> /sw64/lib/perl5/darwin /Library/Perl/Updates/5.10.0 >> /System/Library/Perl/5.10.0/darwin-thread-multi-2level >> /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level >> /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level >> /Network/Library/Perl/5.10.0 /Network/Library/Perl >> /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level >> /System/Library/Perl/Extras/5.10.0 .) at >> /sw64/share/xtal/aline_011208/bin/aline line 37. >> BEGIN failed--compilation aborted at >> /sw64/share/xtal/aline_011208/bin/aline line 37. >> s...@host005:~> >> >> I even tried with the >> >> perl -MCPAN -e 'install Tk' >> >> command, as suggested by the website, but nothing changed. >> >> Any idea of what's wrong here? >> Thanks a lot for the tips, >> ciao >> s >> >> On May 25, 2010, at 5:47 AM, Charlie Bond wrote: >> >> > Hi Victor, >> > Thanks for recommending ALINE. >> > >> > It is not exactly true that development has stopped. It is just >> glacially slow as funding for such utilities is not easily obtained! >> > >> > Recommendations for improvements (to improve that potential) are >> well-received and a keen user can write their own plug-ins to achieve new >> functionality. >> > >> > Cheers, >> > Charlie >> > >> > Victor Alves wrote: >> >> Hi Mohd >> >> You can also check: ALINE (An Extensible WYSIWYG Protein Sequence >> Alignment Editor for Publication Quality Figures) >> >> http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/ >> >> It’s quite nice and has a lot of potential, although unfortunately it >> seems that development of the software as stopped :-( >> >> Cheers >> >> Victor Alves >> >> *From:* CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] *On >> Behalf Of *Salameh, Mohd A., Ph.D. >> >> *Sent:* sexta-feira, 21 de Maio de 2010 16:11 >> >> *To:* CCP4BB@JISCMAIL.AC.UK >> >> *Subject:* [ccp4bb] Alignment software >> >> Dear All, >> >> I’m trying to prepare an alignment figure of 2 proteins that highlight >> conserved and similar residues and probably secondary structures; I will >> greatly appreciate it if anybody can recommend a software that I can use. >> Thanks, Mohd >> > >> > -- >> > Charlie Bond >> > Professorial Fellow >> > University of Western Australia >> > School of Biomedical, Biomolecular and Chemical Sciences >> > M310 >> > 35 Stirling Highway >> > Crawley WA 6009 >> > Australia >> > charles.b...@uwa.edu.au >> > +61 8 6488 4406 >> >> >> -- >> Sebastiano Pasqualato, PhD >> IFOM-IEO Campus >> Dipartimento di Oncologia Sperimentale >> Istituto Europeo di Oncologia >> via Adamello, 16 >> 20139 - Milano >> Italy >> >> tel +39 02 9437 5094 >> fax +39 02 9437 5990 >> > > > > -- > Roger B. Dodd, PhD. > Cambridge Institute for Medical Research > Wellcome Trust/MRC Building > Hills Road > Cambridge > CB2 0XY > UK > > > > -- > > Sebastiano Pasqualato, PhD > IFOM-IEO Campus > Dipartimento di Oncologia Sperimentale > Istituto Europeo di Oncologia > via Adamello, 16 > 20139 - Milano > Italy > > tel +39 02 9437 5094 > fax +39 02 9437 5990 > >
