I used Mugsy for multiple alignment. Now I want to convert an output MAF file to a fasta file. I know that mugsy provides a maf2fasta.pl script but I don't understand how to use it (I don't know Perl). In the description of the script it says that it should be called this way:
./maf2fasta.pl [label] < maf > fasta
Does it mean I need to provide maf file and the name of the output fasta file or I need to provide the names of the input fasta files with genomes? The script doesn't print anything so I can't understand what's going on there.
Or maybe someone knows other ways to convert MAF to fasta?