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Converting MAF to Fasta

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?

fasta maf alignment mugsy
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written by little_more • little_more

OK, let your maf file called myfile.maf and we want the output fatsa file to be myfile.fasta

Then we use this command:

./maf2fasta.pl < myfile.maf > myfile.fasta

Similar question:
Convert MAF to FASTA

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written by Medhat Medhat

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