needleall - Many-to-many pairwise alignments of two sequence sets

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EMBOSS 6.4.0                                       05/11/2012                                      NEEDLEALL(1e)

needleall is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”).
       It is part of the "Alignment:Global" command group(s).

       needleall - Many-to-many pairwise alignments of two sequence sets

Inputsection-asequenceseqset-bsequenceseqall-datafilematrixf
           This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62'
           (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data'
           directory of the EMBOSS installation.

   Requiredsection-gapopenfloat
           The gap open 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: @($(acdprotein)? 10.0 :
           10.0 )

       -gapextendfloat
           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: @($(acdprotein)? 0.5 : 0.5 )

   Additionalsection-endweightboolean
           Default value: N

       -endopenfloat
           The end gap open penalty is the score taken away when an end 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: @($(acdprotein)?
           10.0 : 10.0 )

       -endextendfloat
           The end gap extension, penalty is added to the end gap penalty for each base or residue in the end
           gap. Default value: @($(acdprotein)? 0.5 : 0.5 )

       -minscorefloat
           Minimum alignment score to report an alignment.

   Outputsection-briefboolean
           Brief identity and similarity Default value: Y

       -outfilealign-errorfileoutfile
           Error file to be written to Default value: needleall.error

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

needleall-asequenceseqset-bsequenceseqall [-datafilematrixf] -gapopenfloat-gapextendfloat
                 [-endweightboolean] [-endopenfloat] [-endextendfloat] [-minscorefloat] -briefboolean-outfilealign [-errorfileoutfile]

       needleall-help