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[modeller_usage] Alignmnet format conversion

i have some 200 alignments (for 200 proteins) in Blast output format....as i have to model the query proteins, i want the alignment in PIR format.....Is there any converter that does this??
that does this from command line and not manual submission......

i tried using many tools, but ended in no result or no command line version.....

I also want to know Aln to Pir converter for linux machine.....i wanna use command line for the conversion

Please suggest for both the doubts