I have a set of files with the following extension

```
  A.fa
  A_cod.fa
  B.fa
  B_cod.fa
  C.fa
  C_cod.fa
  D.fa
  D_cod.fa

```

For each file I had to do it as

```
 prank -convert -d=A.fa -dna=A_cod.fa -o=A.alignment -keep

```

I wanted to loop over the set of files and do the above instead of each file and tried:

```
  for f in *.fa and for f1 in *_cod.fa; do prank -convert -d=$f -dna=$f1 -o=$f.alignment -keep; done ;

```

But this does not work. So for each file A -d should read in .fa file and -dna should read in the corresponding \_cod.fa file and simialrly for B and so on.