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I am trying to learn bioinformatics the hard way. I have no background in Linux, Ubuntu, bash, Perl, Python, etc. I'm trying to use several programs, mostly the bioperl modules, that have been installed and used on this machine before.

It seems that older versions function but the newer ones don't. Specifically, it's the NCBI standalone blast group of programs. I can use blastall, but not blastn, fastacmd, or blastdbcmd even though those modules are present and show up as executable. The error I get is no such file or dir.

How do I uninstall this group of modules and then reinstall them? Or is there some other reason why they would not be found? I did try to run them from within the directory where they are located.

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What do you see if you type which <cmd>, e.g. which blastall and which blastn in the terminal? If you have sudo privileges, you could try following BioPerl's installation guide (after you run the which commands). – Ricardo Altamirano Mar 6 '13 at 14:15

They are not supposed to be used as standalone executables. See man bastall for details but, for example:

blastall -p blastn -i input.fa -d nr

will run a blastn search against the nr database using the fasta file input.fa as input. In general, to run any of these programs, you need to run

blastall -p PROGRAM_NAME

Oh, and these are not bioperl modules, they are standalone programs and have nothing to do with bioperl.

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