in reply to Inline::C .h file not generated

Well where is seqaln.h? From the compile line given and assuming it's in the source as #include <seqaln.h>, it needs to be in one of the following directories

There are many ways to find out the default directories, if gcc, just type cpp -v

-derby

update: And if it's not in one of those directories, you'll have to modify your script to tell Inline::C what additional directories to search.

In Section Seekers of Perl Wisdom