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diff --git a/academic/primer3/man1/ntdpal.1 b/academic/primer3/man1/ntdpal.1 new file mode 100644 index 0000000000..3f3cbfe228 --- /dev/null +++ b/academic/primer3/man1/ntdpal.1 @@ -0,0 +1,128 @@ +'\" t +.\" Title: NTDPAL +.\" Author: [FIXME: author] [see http://docbook.sf.net/el/author] +.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/> +.\" Date: 11/30/2011 +.\" Manual: Primer3 User Manuals +.\" Source: ntdpal 1.1.4 +.\" Language: English +.\" +.TH "NTDPAL" "1" "11/30/2011" "ntdpal 1.1.4" "Primer3 User Manuals" +.\" ----------------------------------------------------------------- +.\" * Define some portability stuff +.\" ----------------------------------------------------------------- +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.\" http://bugs.debian.org/507673 +.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html +.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" ----------------------------------------------------------------- +.\" * set default formatting +.\" ----------------------------------------------------------------- +.\" disable hyphenation +.nh +.\" disable justification (adjust text to left margin only) +.ad l +.\" ----------------------------------------------------------------- +.\" * MAIN CONTENT STARTS HERE * +.\" ----------------------------------------------------------------- +.SH "NAME" +ntdpal \- Provides Primer3\*(Aqs alignment functionality +.SH "SYNOPSIS" +.HP \w'\fBntdpal\fR\ 'u +\fBntdpal\fR [\-g\ \fIgval\fR] [\-l\ \fIlval\fR] [\-m\ \fImval\fR] [\-f1,\ f2,\ f3] [\-p] [\-s] [\-e] {\fIseq1\fR} {\fIseq2\fR} {\fImode\fR} +.SH "DESCRIPTION" +.PP +Ntdpal (NucleoTide Dynamic Programming ALignment) is a stand\-alone program that provides Primer3\*(Aqs alignment functionality (local, a\&.k\&.a\&. Smith\-Waterman, global, a\&.k\&.a\&. Needleman\-Wunsch, plus "half global")\&. +.SH "OPTIONS" +.PP +\fB\-g\fR \fIgval\fR +.RS 4 +\fIgval\fR +is a (positive) float (\&.01 precision) specifying penalty for creating a gap respectively (the penalties are subtracted from the output score) +.RE +.PP +\fB\-l\fR \fIval\fR +.RS 4 +\fIlval\fR +is a (positive) float (\&.01 precision) specifying penalty for lengthening a gap respectively (the penalties are subtracted from the output score) +.RE +.PP +\fB\-a\fR +.RS 4 +Causes the scoring matrix to be modified by dpal_set_ambiguity_codes\&. +.RE +.PP +\fB\-e\fR +.RS 4 +Causes the end position of the alignment in both sequences to be printed\&. Do not confuse with the \*(Aqe\*(Aq +\fImode\fR\&. +.RE +.PP +\fB\-f1, \-f2, \-f3\fR +.RS 4 +Force specific implementations\&. \-f2 forces use an implementation that might provide more informative error messages, possibly at the expense of some speed\&. +.RE +.PP +\fB\-h\fR +.RS 4 +Use a different scoring matrix: G and C matches = 3, A and T = 2, and mismatches = \-0\&.5\&. (The default scoring matrix assigns 1 to a match, and \-1 to a mismatch\&.) +.RE +.PP +\fB\-p\fR +.RS 4 +Causes the alignment to be displayed on stderr\&. +.RE +.PP +\fB\-s\fR +.RS 4 +causes +\fIonly\fR +the score to printed\&. +.RE +.PP +\fB\-m\fR \fImval\fR +.RS 4 +is the maximum allowed gap (default is 3)\&. +.RE +.PP +\fIseq1\fR and \fIseq2\fR +.RS 4 +are the sequences to be aligned\&. +.RE +.PP +\fImode\fR +.RS 4 +is one of +\fIg\fR, +\fIG\fR, +\fIl\fR, or +\fIL\fR +specifying a global, global end\-anchored, local, or local end\-anchored alignment respectively\&. For backward compatibility +\fIe\fR +is equivalent to +\fIG\fR\&. +.RE +.SH "REFERENCE" +.PP +Please cite Rozen, S\&., Skaletsky, H\&. "Primer3 on the WWW for general users and for biologist programmers\&." In S\&. Krawetz and S\&. Misener, eds\&. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology\&. Humana Press, Totowa, NJ, 2000, pages 365\-386\&. +.SH "SEE ALSO" +.PP + +\fBprimer3_core\fR(1) +\fBoligotm\fR(1) +.SH "COPYRIGHT" +.br +Copyright \(co 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008 Whitehead Institute for Biomedical Research, Steve Rozen (http://jura.wi.mit.edu/rozen), Helen Skaletsky +.br +.PP +All rights reserved\&. On Debian\-based systems, please consult +/usr/share/doc/primer3/copyright +to read the licence of ntdpal\&. +.PP +This manual page was written by Charles Plessy <plessy@debian\&.org> for the +Debian(TM) +system (but may be used by others)\&. Permission is granted to copy, distribute and/or modify this document under the same terms as oligotm itself\&. + +.sp |