academic/primer3: Updated for version 2.4.0.

Signed-off-by: David Spencer <idlemoor@slackbuilds.org>

4 files changed, 423 insertions, 0 deletions

diff --git a/academic/primer3/man1/ntdpal.1 b/academic/primer3/man1/ntdpal.1
new file mode 100644
index 0000000000000..3f3cbfe228570
--- /dev/null
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+'\" 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
diff --git a/academic/primer3/man1/ntthal.1 b/academic/primer3/man1/ntthal.1
new file mode 100644
index 0000000000000..e3e5e8888a08f
--- /dev/null
+++ b/academic/primer3/man1/ntthal.1
@@ -0,0 +1,40 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.43.3.
+.TH NTTHAL "1" "December 2013" "2.3.6" "Primer3 User Manuals"
+.SH NAME
+ntthal \- Provides Primer3's alignment functionality based on nearest-neighbor thermodynamical approach
+.SH DESCRIPTION
+\fBntthal\fR is analogous to \fBntdpal\fR.  Between two sequences, \fBntthal\fR finds
+alignment/sec structure, that has the highest melting
+temperature. Ntthal is based on nearest-neighbor thermodynamical
+approach.
+.SH SYNOPSIS
+.B ntthal
+\fIOPTIONS\fR oligo
+.SH OPTIONS
+\fB\-mv\fR monovalent_conc  \- concentration of monovalent cations in mM, by default 50 mM
+.PP
+\fB\-dv\fR divalent_conc    \- concentration of divalent cations in mM, by default 0 mM
+.PP
+\fB\-n\fR  dNTP_conc        \- concentration of deoxynycleotide triphosphate in mM, by default 0 mM
+.PP
+\fB\-d\fR  dna_conc         \- concentration of DNA strands in nM, by default 50 nM
+.PP
+\fB\-a\fR  mode             \- alignment type, END1, END2, ANY and HAIRPIN, by default ANY (when duplex)
+.PP
+\fB\-t\fR  temp             \- temperature at which duplex is calculated, by default 37C
+.PP
+\fB\-r\fR                   \- causes the alignment NOT to be displayed on stderr, _only_ Tm is printed
+.PP
+\fB\-maxloop\fR size        \- the maximum size of secondary structures loops.
+.IP
+Default is 30 (this is maximum allowed length, currently).
+.PP
+\fB\-path\fR <path>         \- the path to the thermodynamic parameter files
+.PP
+\fB\-s1\fR DNA_oligomer
+.PP
+\fB\-s2\fR DNA_oligomer
+.SH AUTHORS
+This manual page was created by Andreas Tille <tille@debian.org> using help2man
+for Debian but can be freely used for any other purpose
+
diff --git a/academic/primer3/man1/oligotm.1 b/academic/primer3/man1/oligotm.1
new file mode 100644
index 0000000000000..ed9dcf7910d7b
--- /dev/null
+++ b/academic/primer3/man1/oligotm.1
@@ -0,0 +1,165 @@
+'\" t
+.\"     Title: OLIGOTM
+.\"    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: oligotm 1.1.4
+.\"  Language: English
+.\"
+.TH "OLIGOTM" "1" "11/30/2011" "oligotm 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"
+oligotm \- Prints oligo\*(Aqs melting temperature on stdout
+.SH "SYNOPSIS"
+.HP \w'\fBoligotm\fR\ 'u
+\fBoligotm\fR [OPTIONS] {oligo}
+.PP
+where oligo is a DNA sequence of between 2 and 36 bases
+.SH "DESCRIPTION"
+.PP
+
+\fBoligotm\fR
+prints the melting temperature of a given deoxyribonucleotide on the standard output\&. It is part of the oligotm library\&.
+.SH "OPTIONS"
+.PP
+\fB\-mv\fR \fImonovalent_conc\fR
+.RS 4
+Concentration of monovalent cations in mM, by default 50\ \&mM\&.
+.RE
+.PP
+\fB\-dv\fR \fIdivalent_conc\fR
+.RS 4
+Concentration of divalent cations in mM, by default 0\ \&mM\&.
+.RE
+.PP
+\fB\-n\fR \fIdNTP_conc\fR
+.RS 4
+Concentration of deoxynucleotide triphosphate in mM, by default 0\ \&mM\&.
+.RE
+.PP
+\fB\-d\fR \fIdna_conc\fR
+.RS 4
+Concentration of DNA strands in nM, by default 50\ \&nM\&.
+.RE
+.PP
+\fB\-tp\fR \fI[0|1]\fR
+.RS 4
+Specifies the table of thermodynamic parameters and the method of melting temperature calculation:
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+\fI0\fR
+Breslauer et al\&., 1986 and Rychlik et al\&., 1990 (used by primer3 up to and including release 1\&.1\&.0)\&. This is the default, but
+\fInot\fR
+the recommended value\&.
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+\fI1\fR
+Use nearest neighbor parameter from SantaLucia 1998\&.
+\fIThis is the recommended value\fR\&.
+.RE
+.RE
+.PP
+\fB\-sc\fR \fI[0\&.\&.2]\fR
+.RS 4
+Specifies salt correction formula for the melting temperature calculation:
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+\fI0\fR
+Schildkraut and Lifson 1965, used by primer3 up to and including release 1\&.1\&.0\&. This is the default, but
+\fInot\fR
+the recommended value\&.
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+\fI1\fR
+SantaLucia 1998\&.
+\fIThis is the recommended value\fR\&.
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+\fI2\fR
+Owczarzy et al\&., 2004\&.
+.RE
+.RE
+.PP
+\fB\-i\fR
+.RS 4
+prints references to publications which were used for thermodynamic calculations\&.
+.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)
+\fBntdpal\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 oligotm\&.
+.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
diff --git a/academic/primer3/man1/primer3_core.1 b/academic/primer3/man1/primer3_core.1
new file mode 100644
index 0000000000000..aa99059dc6d8d
--- /dev/null
+++ b/academic/primer3/man1/primer3_core.1
@@ -0,0 +1,90 @@
+.\"     Title: PRIMER3_CORE
+.\"    Author: 
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\"      Date: 05/09/2008
+.\"    Manual: Primer3 User Manuals
+.\"    Source: primer3_core 1.1.4
+.\"
+.TH "PRIMER3_CORE" "1" "05/09/2008" "primer3_core 1.1.4" "Primer3 User Manuals"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+primer3_core \- Designs primers for PCR
+.SH "SYNOPSIS"
+.HP 13
+\fBprimer3_core\fR [\-format_output] [\-strict_tags] [<\ \fIinput_file\fR]
+.SH "DESCRIPTION"
+.PP
+primer3_core picks primers for PCR reactions, considering as criteria oligonucleotide melting temperature, size, GC content and primer\-dimer possibilities, PCR product size, positional constraints within the source sequence, and miscellaneous other constraints\&.
+.PP
+By default, primer3_core accepts input and produces output in Boulder\-io format, a pre\-XML text\-based input/output format for program\-to\-program data interchange format\&. The Boulder\-io format and the commands that primer3_core understands are described in the
+\fIREADME\fR
+file, which on Debian systems can be found in
+\fI/usr/share/doc/primer3/\fR\&.
+.SH "OPTIONS"
+.PP
+\fB\-format_output\fR
+.RS 4
+Prints a more user\-oriented report for each sequence\&.
+.RE
+.PP
+\fB\-strict_tags\fR
+.RS 4
+primer3_core echoes and ignores any tags it does not recognize, unless the
+\fB\-strict_tags\fR
+flag is set on the command line, in which case primer3_core prints an error in the PRIMER_ERROR output tag, and prints additional information on stdout; this option can be useful for debugging systems that incorporate primer\&.
+.RE
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+Note
+.PP
+The old flag \-2x_compat is no longer supported\&.
+.SH "EXIT STATUS CODES"
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'0 on normal operation\&.
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'\-1 under the following conditions: illegal command\-line arguments, unable to fflush stdout, unable to open (for writing and creating) a \&.for, \&.rev or \&.int file (probably due to a protection problem)\&.
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'\-2 on out\-of\-memory\&.
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'\-3 empty input\&.
+.RE
+.sp
+.RS 4
+\h'-04'\(bu\h'+03'\-4 error in a "Global" input tag (message in PRIMER_ERROR)\&.
+.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
+
+\fBntdpal\fR(1)
+\fBoligotm\fR(1)
+.SH "COPYRIGHT"
+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
+\fI/usr/share/doc/primer3/copyright\fR
+to read the licence of primer3_core\&.
+.PP
+This manual page was written by Steffen Moeller
+<moeller@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 primer3_core itself\&.
+
+.sp