Author: malex-guest Date: 2011-03-07 16:03:21 +0000 (Mon, 07 Mar 2011) New Revision: 6183
Added: trunk/packages/seq-gen/trunk/debian/seq-gen.1 Modified: trunk/packages/seq-gen/trunk/debian/control trunk/packages/seq-gen/trunk/debian/copyright trunk/packages/seq-gen/trunk/debian/rules trunk/packages/seq-gen/trunk/debian/seq-gen-doc.install Log: manual page , copyright & minor changes. Modified: trunk/packages/seq-gen/trunk/debian/control =================================================================== --- trunk/packages/seq-gen/trunk/debian/control 2011-03-07 16:01:48 UTC (rev 6182) +++ trunk/packages/seq-gen/trunk/debian/control 2011-03-07 16:03:21 UTC (rev 6183) @@ -27,4 +27,9 @@ Package: seq-gen-doc Architecture: all Description: documentation for seq-gen + Seq-Gen is a program that will simulate the evolution of nucleotide + or amino acid sequences along a phylogeny, using common models of the + substitution process. + . + This package contains the documentation for seq-gen Modified: trunk/packages/seq-gen/trunk/debian/copyright =================================================================== --- trunk/packages/seq-gen/trunk/debian/copyright 2011-03-07 16:01:48 UTC (rev 6182) +++ trunk/packages/seq-gen/trunk/debian/copyright 2011-03-07 16:03:21 UTC (rev 6183) @@ -3,10 +3,42 @@ Source: <url://example.com> Files: * -Copyright: <years> <put author's name and email here> - <years> <likewise for another author> -License: GPL-3.0+ +Copyright: Copyright (c)1996-2004, Andrew Rambaut & Nick Grassly + Department of Zoology, University of Oxford + All rights reserved. +License: + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + 1. Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + + 2. Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in the + documentation and/or other materials provided with the distribution. + + 3. The names of its contributors may not be used to endorse or promote + products derived from this software without specific prior written + permission. + + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT + LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR + A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR + CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, + EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, + PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR + PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF + LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING + NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS + SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + Any feedback is very welcome. + http://evolve.zoo.ox.ac.uk/software/Seq-Gen/ + email: [email protected] + Files: debian/* Copyright: 2011 Alex Mestiashvili <[email protected]> License: GPL-3.0+ @@ -27,14 +59,3 @@ . On Debian systems, the complete text of the GNU General Public License version 3 can be found in "/usr/share/common-licenses/GPL-3". - -# Please choose a license for your packaging work. If the program you package -# uses a mainstream license, using the same license is the safest choice. -# Please avoid to pick license terms that are more restrictive than the -# packaged work, as it may make Debian's contributions unacceptable upstream. -# If you just want it to be GPL version 3, leave the following line in. - -and is licensed under the GPL version 3, see above. - -# Please also look if there are files or directories which have a -# different copyright/license attached and list them here. Modified: trunk/packages/seq-gen/trunk/debian/rules =================================================================== --- trunk/packages/seq-gen/trunk/debian/rules 2011-03-07 16:01:48 UTC (rev 6182) +++ trunk/packages/seq-gen/trunk/debian/rules 2011-03-07 16:03:21 UTC (rev 6183) @@ -10,3 +10,6 @@ %: dh $@ --sourcedirectory=source + +override_dh_installchangelogs: + dh_installchangelogs documentation/Using_Seq-Gen_with_PAUP Modified: trunk/packages/seq-gen/trunk/debian/seq-gen-doc.install =================================================================== --- trunk/packages/seq-gen/trunk/debian/seq-gen-doc.install 2011-03-07 16:01:48 UTC (rev 6182) +++ trunk/packages/seq-gen/trunk/debian/seq-gen-doc.install 2011-03-07 16:03:21 UTC (rev 6183) @@ -1 +1,3 @@ -#DOCS# +documentation/Seq-Gen.Manual.html usr/share/doc/seq-gen/ +documentation/Using_Seq-Gen_with_PAUP usr/share/doc/seq-gen/ + Added: trunk/packages/seq-gen/trunk/debian/seq-gen.1 =================================================================== --- trunk/packages/seq-gen/trunk/debian/seq-gen.1 (rev 0) +++ trunk/packages/seq-gen/trunk/debian/seq-gen.1 2011-03-07 16:03:21 UTC (rev 6183) @@ -0,0 +1,81 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2. +.TH SEQ-GEN "1" "March 2011" "seq-gen 1.3.2" "User Commands" +.SH NAME +seq-gen \- Sequence Generator +.SH SYNOPSIS +.B seq-gen +[\fI-m MODEL\fR] [\fI-l #\fR] [\fI-n #\fR] [\fI-p #\fR] [\fI-s # | -d #\fR] [\fI-k #\fR][\-c #1 #2 #3 | \-a\fR # [\-g #]] [\-f e | #] [\-t # | \-r\fR #][\-z #] [\-o[p][r][n]] [\-w[a][r]] [\-x NAME] [\-q] [\-h] [treefile] +.SH DESCRIPTION +Sequence Generator \- seq\-gen +Version 1.3.2 +.IP +.HP +\fB\-l\fR: # = sequence length [default = 1000]. +.HP +\fB\-n\fR: # = simulated datasets per tree [default = 1]. +.HP +\fB\-p\fR: # = number of partitions (and trees) per sequence [default = 1]. +.HP +\fB\-s\fR: # = branch length scaling factor [default = 1.0]. +.HP +\fB\-d\fR: # = total tree scale [default = use branch lengths]. +.HP +\fB\-k\fR: # = use sequence k as ancestral (needs alignment) [default = random]. +.IP +Substitution model options: +.HP +\fB\-m\fR: MODEL = HKY, F84, GTR, JTT, WAG, PAM, BLOSUM, MTREV, GENERAL +.IP +HKY, F84 & GTR are for nucleotides the rest are for amino acids +.HP +\fB\-a\fR: # = shape (alpha) for gamma rate heterogeneity [default = none]. +.HP +\fB\-g\fR: # = number of gamma rate categories [default = continuous]. +.HP +\fB\-i\fR: # = proportion of invariable sites [default = 0.0]. +.IP +Nucleotid model specific options: +.HP +\fB\-c\fR: #1 #2 #3 = rates for codon position heterogeneity [default = none]. +.HP +\fB\-t\fR: # = transition\-transversion ratio [default = equal rate]. +.HP +\fB\-r\fR: #1 #2 #3 #4 #5 #6= general rate matrix [default = all 1.0]. +.HP +\fB\-f\fR: #A #C #G #T = nucleotide frequencies [default = all equal]. +.IP +Amino Acid model specific options: +.IP +specify using the order ARNDCQEGHILKMFPSTWYV +.HP +\fB\-r\fR: #1 .. #190 = general rate matrix [default = all 1.0]. +.HP +\fB\-f\fR: #1 .. #20 = amino acid frequencies e=equal [default = matrix freqs]. +.IP +Miscellaneous options: +.HP +\fB\-z\fR: # = seed for random number generator [default = system generated]. +.HP +\fB\-o\fR: Output file format [default = PHYLIP] +.IP +p PHYLIP format +r relaxed PHYLIP format +n NEXUS format +.HP +\fB\-w\fR: Write additional information [default = none] +.IP +a Write ancestral sequences for each node +r Write rate for each site +.HP +\fB\-x\fR: NAME = a text file to insert after every dataset [default = none]. +.HP +\fB\-h\fR: Give this help message +.HP +\fB\-q\fR: Quiet +.IP +treefile: name of tree file [default = trees on stdin] +.SH AUTHOR +(c) Copyright, 1996\-2004 Andrew Rambaut and Nick Grassly +Department of Zoology, University of Oxford +South Parks Road, Oxford OX1 3PS, U.K. + _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
