allversusall - Sequence similarity data from all-versus-all comparison.

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DOMALIGN 0.1.0+20100721                            08/11/2010                                   ALLVERSUSALL(1e)

allversusall is a command line program from EMBOSS (“the European Molecular Biology Open Software
       Suite”). It is part of the "Utils:Database creation" command group(s).

       allversusall - Sequence similarity data from all-versus-all comparison.

Inputsection-seqinpathdirlist
           Default value: ./

       -matrixmatrixf
           This option specifies the residue substitution matrix that is used for sequence comparison. Default
           value: EBLOSUM62

   RequiredsectionAdditionalsection-gapopenfloat
           This option specifies the gap insertion penalty. The gap insertion penalty is the score taken away
           when a gap is created. The best value depends on the choice of comparison matrix. The default value
           assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for
           nucleotide sequences. Default value: 10

       -gapextendfloat
           This option specifies the gap extension penalty. The gap extension, penalty is added to the standard
           gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you
           will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower
           than the gap penalty. An exception is where one or both sequences are single reads with possible
           sequencing errors in which case you would expect many single base gaps. You can get this result by
           setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap
           scoring. Default value: 0.5

   Outputsection-datoutdiroutdir
           This option specifies the location of sequence similarity data files (output). Default value: ./

       -logfileoutfile
           This option specifies the name of ALLVERSUSALL log file (output). The log file contains messages
           about any errors arising while ALLVERSUSALL ran. Default value: allversusall.log

       allversusall is fully documented via the tfm(1) system.

allversusall-seqinpathdirlist [-matrixmatrixf] [-gapopenfloat] [-gapextendfloat] -datoutdiroutdir-logfileoutfileallversusall-help