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.\"     Title: NEEDLEALL
.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
.\"      Date: 05/11/2012
.\"    Manual: EMBOSS Manual for Debian
.\"    Source: EMBOSS 6.4.0
.\"  Language: English
.\"
.TH "NEEDLEALL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
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.SH "NAME"
needleall \- Many\-to\-many pairwise alignments of two sequence sets
.SH "SYNOPSIS"
.HP \w'\fBneedleall\fR\ 'u
\fBneedleall\fR \fB\-asequence\ \fR\fB\fIseqset\fR\fR \fB\-bsequence\ \fR\fB\fIseqall\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-gapopen\ \fR\fB\fIfloat\fR\fR \fB\-gapextend\ \fR\fB\fIfloat\fR\fR [\fB\-endweight\ \fR\fB\fIboolean\fR\fR] [\fB\-endopen\ \fR\fB\fIfloat\fR\fR] [\fB\-endextend\ \fR\fB\fIfloat\fR\fR] [\fB\-minscore\ \fR\fB\fIfloat\fR\fR] \fB\-brief\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIalign\fR\fR [\fB\-errorfile\ \fR\fB\fIoutfile\fR\fR]
.HP \w'\fBneedleall\fR\ 'u
\fBneedleall\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBneedleall\fR
is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Global" command group(s)\&.
.SH "OPTIONS"
.SS "Input section"
.PP
\fB\-asequence\fR \fIseqset\fR
.RS 4
.RE
.PP
\fB\-bsequence\fR \fIseqall\fR
.RS 4
.RE
.PP
\fB\-datafile\fR \fImatrixf\fR
.RS 4
This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&.
.RE
.SS "Required section"
.PP
\fB\-gapopen\fR \fIfloat\fR
.RS 4
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: @($(acdprotein)? 10\&.0 : 10\&.0 )
.RE
.PP
\fB\-gapextend\fR \fIfloat\fR
.RS 4
The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps\&. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring\&. Default value: @($(acdprotein)? 0\&.5 : 0\&.5 )
.RE
.SS "Additional section"
.PP
\fB\-endweight\fR \fIboolean\fR
.RS 4
Default value: N
.RE
.PP
\fB\-endopen\fR \fIfloat\fR
.RS 4
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: @($(acdprotein)? 10\&.0 : 10\&.0 )
.RE
.PP
\fB\-endextend\fR \fIfloat\fR
.RS 4
The end gap extension, penalty is added to the end gap penalty for each base or residue in the end gap\&. Default value: @($(acdprotein)? 0\&.5 : 0\&.5 )
.RE
.PP
\fB\-minscore\fR \fIfloat\fR
.RS 4
Minimum alignment score to report an alignment\&.
.RE
.SS "Output section"
.PP
\fB\-brief\fR \fIboolean\fR
.RS 4
Brief identity and similarity Default value: Y
.RE
.PP
\fB\-outfile\fR \fIalign\fR
.RS 4
.RE
.PP
\fB\-errorfile\fR \fIoutfile\fR
.RS 4
Error file to be written to Default value: needleall\&.error
.RE
.SH "BUGS"
.PP
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)\&.
.SH "SEE ALSO"
.PP
needleall is fully documented via the
\fBtfm\fR(1)
system\&.
.SH "AUTHOR"
.PP
\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
.SH "COPYRIGHT"
.br
.PP
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\&.
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