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


allversusall -seqinpath dirlist [-matrix matrixf] [-gapopen float] [-gapextend float]
-datoutdir outdir -logfile outfile

allversusall -help


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).


Input section
-seqinpath dirlist
Default value: ./

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

Required section
Additional section
-gapopen float
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

-gapextend float
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

Output section
-datoutdir outdir
This option specifies the location of sequence similarity data files (output). Default
value: ./

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

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