Man pages sections > man1 > edialign

edialign - Local multiple alignment of sequences

EDIALIGN(1e) EMBOSS Manual for Debian EDIALIGN(1e)

NAME

edialign - Local multiple alignment of sequences

SYNOPSIS

edialign -sequences seqset -nucmode list -revcomp boolean [ -overlapw selection] [-linkage  list] [-maxfragl integer] -fragmat boolean -fragsim integer [ -itscore boolean] [-threshold  float] -mask boolean -dostars boolean -starnum integer -outfile outfile -outseq seqoutall
edialign -help

DESCRIPTION

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

OPTIONS

Input section

-sequences seqset

Additional section

-nucmode list
Nucleic acid sequence alignment mode (simple, translated or mixed) Default value: n
-revcomp boolean
Default value: N
-overlapw selection
By default overlap weights are used when Nseq =<35 but you can set this to 'yes' or 'no' Default value: default (when Nseq =< 35)
-linkage list
Clustering method to construct sequence tree (UPGMA, minimum linkage or maximum linkage) Default value: UPGMA
-maxfragl integer
Default value: 40
-fragmat boolean
Default value: N
-fragsim integer
Default value: 4
-itscore boolean
Default value: N
-threshold float
Default value: 0.0

Output section

-mask boolean
Default value: N
-dostars boolean
Default value: N
-starnum integer
Default value: 4
-outfile outfile
-outseq seqoutall

BUGS

Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031).

SEE ALSO

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

AUTHOR

Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Wrote the script used to autogenerate this manual page.
This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.
 
05/11/2012 EMBOSS 6.4.0