StrAl: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time.
See Dalli et al. (2006) for more info
This is a near exact copy of StrAl 0.5.4 to make sure the code survives and is compileable. The original is / used to be available at http://www.biophys.uni-duesseldorf.de/stral/
Differences from the original 0.5.4:
- All precompiled libraries removed
- libweighbor only used if found at configure time
StrAl requires ViennaRNA (version 1.8; not 2!), Sean Eddy's Squid library
1.9g and the Mhash library to be installed beforehand. You can find copies of
versions which are known to work in the third-party folder of Stral's source code.
For each package, use the GNU triple jump to install it:
./configure && make && sudo make install. If you are not root, use
./configure --prefix SOMEPATH to install the packages to SOMEPATH
you have access to. In that case, let Stral's configure
know about the path by modifying LDFLAGS and CFLAGS on the commandline.
This is done by setting the CFLAGS and LDFLAGS environment variables.
For example, if you installed packages to $HOME/local run
export CFLAGS="-I$HOME/local and export LDFLAGS="-L$HOME/local/
before running ./configure.
Notes on ViennaRNA: On OsX, if you get "ld: symbol(s) not found for architecture x86_64" while compiling/installing ViennaRNA try a newer
GCC (setting CC to gcc-mp-4.8 worked for me) or experiment with
ARCHFLAGS="-arch x86_64" and --disable-openmp as options to configure.
After a first checkout you will need to setup automake once:
$ ./bootstrap
If you see correspondong warnings you might also need to run:
$ automake --add-missing
Should ltmain.sh be mising please also run:
$ [g]libtoolize && ./bootstrap
After that configure and Makefile.in's will have been generated and you can do the GNU triple jump:
$ ./configure
$ make
$ make install