In order to run ./configure; make; make install, you need at least a working POSIX-compatible shell, a compatible version of Make and a working compiler. I'm not sure whether ppm install MinGW provides a POSIX shell (bin/sh or bin/bash); shell is not provided by default in Strawberry Perl.

Try installing MinGW (is you use ActivePerl), MSYS, adding its bin directory to the PATH environment variable and running sh configure. Maybe it will run properly and create the Makefiles to run make on.

You can also install Cygwin which can download all the necessary utilities (bash, automake, make, gcc, perl) by itself (and for itself) and build the required program just like under Linux.

Sorry if my advice was wrong.

In reply to Re: Installing and using RNAfold in Windows by aitap
in thread Installing and using RNAfold in Windows by eupath

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