--- wise-2.4.1.orig/debian/manpages.d/Makefile
+++ wise-2.4.1/debian/manpages.d/Makefile
@@ -0,0 +1,13 @@
+SHELL = /bin/sh
+
+MANPAGES = dba.1 dnal.1 estwise.1 estwisedb.1 genewise.1 genewisedb.1 genomewise.1 promoterwise.1 psw.1 pswdb.1 scanwise.1 scanwise_server.1
+
+all: $(MANPAGES)
+
+$(MANPAGES): %.1 : %.sgml
+ docbook-to-man $< > $@
+
+clean:
+ $(RM) $(MANPAGES)
+
+.PHONY: all
--- wise-2.4.1.orig/debian/manpages.d/scanwise.sgml
+++ wise-2.4.1/debian/manpages.d/scanwise.sgml
@@ -0,0 +1,144 @@
+ manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+
+
+ Philipp">
+ Benner">
+
+ July 2006">
+
+ 1">
+ mail@philipp-benner.de">
+
+ SCANWISE">
+
+
+ Debian">
+ GNU">
+ GPL">
+]>
+
+
+
+
+ &dhemail;
+
+
+ &dhfirstname;
+ &dhsurname;
+
+
+ 2007
+ &dhusername;
+
+ &dhdate;
+
+
+ &dhucpackage;
+
+ &dhsection;
+
+
+ &dhpackage;
+
+ Fast but sensitive search method for biopolymers
+
+
+
+ &dhpackage;
+
+
+ options
+
+
+
+
+
+ query_sequence_file_fasta
+
+
+
+
+
+ DESCRIPTION
+
+ not available
+
+
+
+ OPTIONS
+
+
+
+
+
+
+ Show summary of options.
+
+
+
+
+
+
+ Show version of program.
+
+
+
+
+
+ SEE ALSO
+
+ dba (1), dnal (1), estwise (1), estwisedb (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise_server (1).
+
+
+ AUTHOR
+
+ This manual page was written by &dhusername; &dhemail; for
+ the &debian; system (but may be used by others). Permission is
+ granted to copy, distribute and/or modify this document under
+ the terms of the &gnu; General Public License, Version 2 any
+ later version published by the Free Software Foundation.
+
+
+ On Debian systems, the complete text of the GNU General Public
+ License can be found in /usr/share/common-licenses/GPL.
+
+
+
+
+
+
+
+
--- wise-2.4.1.orig/debian/manpages.d/estwisedb.sgml
+++ wise-2.4.1/debian/manpages.d/estwisedb.sgml
@@ -0,0 +1,144 @@
+ manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+
+
+ Philipp">
+ Benner">
+
+ July 2006">
+
+ 1">
+ mail@philipp-benner.de">
+
+ ESTWISEDB">
+
+
+ Debian">
+ GNU">
+ GPL">
+]>
+
+
+
+
+ &dhemail;
+
+
+ &dhfirstname;
+ &dhsurname;
+
+
+ 2006
+ &dhusername;
+
+ &dhdate;
+
+
+ &dhucpackage;
+
+ &dhsection;
+
+
+ &dhpackage;
+
+ a database of proteins vs a database of EST/cDNA sequences
+
+
+
+ &dhpackage;
+
+
+ options
+
+
+
+
+
+ protein-input dna-input
+
+
+
+
+
+ DESCRIPTION
+
+ not available
+
+
+
+ OPTIONS
+
+
+
+
+
+
+ Show summary of options.
+
+
+
+
+
+
+ Show version of program.
+
+
+
+
+
+ SEE ALSO
+
+ dba (1), dnal (1), estwise (1), genewise (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1).
+
+
+ AUTHOR
+
+ This manual page was written by &dhusername; &dhemail; for
+ the &debian; system (but may be used by others). Permission is
+ granted to copy, distribute and/or modify this document under
+ the terms of the &gnu; General Public License, Version 2 any
+ later version published by the Free Software Foundation.
+
+
+ On Debian systems, the complete text of the GNU General Public
+ License can be found in /usr/share/common-licenses/GPL.
+
+
+
+
+
+
+
+
--- wise-2.4.1.orig/debian/manpages.d/pswdb.sgml
+++ wise-2.4.1/debian/manpages.d/pswdb.sgml
@@ -0,0 +1,144 @@
+ manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+
+
+ Philipp">
+ Benner">
+
+ July 2006">
+
+ 1">
+ mail@philipp-benner.de">
+
+ PSWDB">
+
+
+ Debian">
+ GNU">
+ GPL">
+]>
+
+
+
+
+ &dhemail;
+
+
+ &dhfirstname;
+ &dhsurname;
+
+
+ 2006
+ &dhusername;
+
+ &dhdate;
+
+
+ &dhucpackage;
+
+ &dhsection;
+
+
+ &dhpackage;
+
+ protein smith waterman database
+
+
+
+ &dhpackage;
+
+
+ options
+
+
+
+
+
+ query_db target_db
+
+
+
+
+
+ DESCRIPTION
+
+ not available
+
+
+
+ OPTIONS
+
+
+
+
+
+
+ Show summary of options.
+
+
+
+
+
+
+ Show version of program.
+
+
+
+
+
+ SEE ALSO
+
+ dba (1), dnal (1), estwise (1), estwisedb (1), genewise (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), scanwise (1), scanwise_server (1).
+
+
+ AUTHOR
+
+ This manual page was written by &dhusername; &dhemail; for
+ the &debian; system (but may be used by others). Permission is
+ granted to copy, distribute and/or modify this document under
+ the terms of the &gnu; General Public License, Version 2 any
+ later version published by the Free Software Foundation.
+
+
+ On Debian systems, the complete text of the GNU General Public
+ License can be found in /usr/share/common-licenses/GPL.
+
+
+
+
+
+
+
+
--- wise-2.4.1.orig/debian/manpages.d/estwise.sgml
+++ wise-2.4.1/debian/manpages.d/estwise.sgml
@@ -0,0 +1,144 @@
+ manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+
+
+ Philipp">
+ Benner">
+
+ July 2006">
+
+ 1">
+ mail@philipp-benner.de">
+
+ ESTWISE">
+
+
+ Debian">
+ GNU">
+ GPL">
+]>
+
+
+
+
+ &dhemail;
+
+
+ &dhfirstname;
+ &dhsurname;
+
+
+ 2006
+ &dhusername;
+
+ &dhdate;
+
+
+ &dhucpackage;
+
+ &dhsection;
+
+
+ &dhpackage;
+
+ comparison of a related protein to cDNA (or ESTs)
+
+
+
+ &dhpackage;
+
+
+ options
+
+
+
+
+
+ protein-file dna-file
+
+
+
+
+
+ DESCRIPTION
+
+ not available
+
+
+
+ OPTIONS
+
+
+
+
+
+
+ Show summary of options.
+
+
+
+
+
+
+ Show version of program.
+
+
+
+
+
+ SEE ALSO
+
+ dba (1), dnal (1), estwisedb (1), genewise (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1).
+
+
+ AUTHOR
+
+ This manual page was written by &dhusername; &dhemail; for
+ the &debian; system (but may be used by others). Permission is
+ granted to copy, distribute and/or modify this document under
+ the terms of the &gnu; General Public License, Version 2 any
+ later version published by the Free Software Foundation.
+
+
+ On Debian systems, the complete text of the GNU General Public
+ License can be found in /usr/share/common-licenses/GPL.
+
+
+
+
+
+
+
+
--- wise-2.4.1.orig/debian/manpages.d/scanwise_server.sgml
+++ wise-2.4.1/debian/manpages.d/scanwise_server.sgml
@@ -0,0 +1,144 @@
+ manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+
+
+ Philipp">
+ Benner">
+
+ July 2006">
+
+ 1">
+ mail@philipp-benner.de">
+
+ SCANWISE_SERVER">
+
+
+ Debian">
+ GNU">
+ GPL">
+]>
+
+
+
+
+ &dhemail;
+
+
+ &dhfirstname;
+ &dhsurname;
+
+
+ 2006
+ &dhusername;
+
+ &dhdate;
+
+
+ &dhucpackage;
+
+ &dhsection;
+
+
+ &dhpackage;
+
+ Server for scanwise
+
+
+
+ &dhpackage;
+
+
+ options
+
+
+
+
+
+ sequence_file_fasta
+
+
+
+
+
+ DESCRIPTION
+
+ not available
+
+
+
+ OPTIONS
+
+
+
+
+
+
+ Show summary of options.
+
+
+
+
+
+
+ Show version of program.
+
+
+
+
+
+ SEE ALSO
+
+ dba (1), dnal (1), estwise (1), estwisedb (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1).
+
+
+ AUTHOR
+
+ This manual page was written by &dhusername; &dhemail; for
+ the &debian; system (but may be used by others). Permission is
+ granted to copy, distribute and/or modify this document under
+ the terms of the &gnu; General Public License, Version 2 any
+ later version published by the Free Software Foundation.
+
+
+ On Debian systems, the complete text of the GNU General Public
+ License can be found in /usr/share/common-licenses/GPL.
+
+
+
+
+
+
+
+
--- wise-2.4.1.orig/debian/manpages.d/dnal.sgml
+++ wise-2.4.1/debian/manpages.d/dnal.sgml
@@ -0,0 +1,144 @@
+ manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+
+
+ Philipp">
+ Benner">
+
+ July 2006">
+
+ 1">
+ mail@philipp-benner.de">
+
+ DNAL">
+
+
+ Debian">
+ GNU">
+ GPL">
+]>
+
+
+
+
+ &dhemail;
+
+
+ &dhfirstname;
+ &dhsurname;
+
+
+ 2006
+ &dhusername;
+
+ &dhdate;
+
+
+ &dhucpackage;
+
+ &dhsection;
+
+
+ &dhpackage;
+
+ ...
+
+
+
+ &dhpackage;
+
+
+ options
+
+
+
+
+
+ dna-file dna-file
+
+
+
+
+
+ DESCRIPTION
+
+ not available
+
+
+
+ OPTIONS
+
+
+
+
+
+
+ Show summary of options.
+
+
+
+
+
+
+ Show version of program.
+
+
+
+
+
+ SEE ALSO
+
+ dba (1), estwise (1), estwisedb (1), genewise (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1).
+
+
+ AUTHOR
+
+ This manual page was written by &dhusername; &dhemail; for
+ the &debian; system (but may be used by others). Permission is
+ granted to copy, distribute and/or modify this document under
+ the terms of the &gnu; General Public License, Version 2 any
+ later version published by the Free Software Foundation.
+
+
+ On Debian systems, the complete text of the GNU General Public
+ License can be found in /usr/share/common-licenses/GPL.
+
+
+
+
+
+
+
+
--- wise-2.4.1.orig/debian/manpages.d/promoterwise.sgml
+++ wise-2.4.1/debian/manpages.d/promoterwise.sgml
@@ -0,0 +1,144 @@
+ manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+
+
+ Philipp">
+ Benner">
+
+ July 2006">
+
+ 1">
+ mail@philipp-benner.de">
+
+ PROMOTERWISE">
+
+
+ Debian">
+ GNU">
+ GPL">
+]>
+
+
+
+
+ &dhemail;
+
+
+ &dhfirstname;
+ &dhsurname;
+
+
+ 2007
+ &dhusername;
+
+ &dhdate;
+
+
+ &dhucpackage;
+
+ &dhsection;
+
+
+ &dhpackage;
+
+ comparison between two promoter sequences
+
+
+
+ &dhpackage;
+
+
+ options
+
+
+
+
+
+ query_sequence target_sequence
+
+
+
+
+
+ DESCRIPTION
+
+ not available
+
+
+
+ OPTIONS
+
+
+
+
+
+
+ Show summary of options.
+
+
+
+
+
+
+ Show version of program.
+
+
+
+
+
+ SEE ALSO
+
+ dba (1), dnal (1), estwise (1), estwisedb (1), genewisedb (1), genomewise (1), psw (1), pswdb (1) scanwise (1) scanwise_server (1).
+
+
+ AUTHOR
+
+ This manual page was written by &dhusername; &dhemail; for
+ the &debian; system (but may be used by others). Permission is
+ granted to copy, distribute and/or modify this document under
+ the terms of the &gnu; General Public License, Version 2 any
+ later version published by the Free Software Foundation.
+
+
+ On Debian systems, the complete text of the GNU General Public
+ License can be found in /usr/share/common-licenses/GPL.
+
+
+
+
+
+
+
+
--- wise-2.4.1.orig/debian/manpages.d/genomewise.sgml
+++ wise-2.4.1/debian/manpages.d/genomewise.sgml
@@ -0,0 +1,144 @@
+ manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+
+
+ Philipp">
+ Benner">
+
+ July 2006">
+
+ 1">
+ mail@philipp-benner.de">
+
+ GENOMEWISE">
+
+
+ Debian">
+ GNU">
+ GPL">
+]>
+
+
+
+
+ &dhemail;
+
+
+ &dhfirstname;
+ &dhsurname;
+
+
+ 2006
+ &dhusername;
+
+ &dhdate;
+
+
+ &dhucpackage;
+
+ &dhsection;
+
+
+ &dhpackage;
+
+ A tool for combining disparate evidence strands
+
+
+
+ &dhpackage;
+
+
+ options
+
+
+
+
+
+ genomic-fasta-file evidence-file
+
+
+
+
+
+ DESCRIPTION
+
+ not available
+
+
+
+ OPTIONS
+
+
+
+
+
+
+ Show summary of options.
+
+
+
+
+
+
+ Show version of program.
+
+
+
+
+
+ SEE ALSO
+
+ dba (1), dnal (1), estwise (1), estwisedb (1), genewise (1), genewisedb (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1).
+
+
+ AUTHOR
+
+ This manual page was written by &dhusername; &dhemail; for
+ the &debian; system (but may be used by others). Permission is
+ granted to copy, distribute and/or modify this document under
+ the terms of the &gnu; General Public License, Version 2 any
+ later version published by the Free Software Foundation.
+
+
+ On Debian systems, the complete text of the GNU General Public
+ License can be found in /usr/share/common-licenses/GPL.
+
+
+
+
+
+
+
+
--- wise-2.4.1.orig/debian/manpages.d/genewise.sgml
+++ wise-2.4.1/debian/manpages.d/genewise.sgml
@@ -0,0 +1,144 @@
+ manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+
+
+ Philipp">
+ Benner">
+
+ July 2006">
+
+ 1">
+ mail@philipp-benner.de">
+
+ GENEWISE">
+
+
+ Debian">
+ GNU">
+ GPL">
+]>
+
+
+
+
+ &dhemail;
+
+
+ &dhfirstname;
+ &dhsurname;
+
+
+ 2006
+ &dhusername;
+
+ &dhdate;
+
+
+ &dhucpackage;
+
+ &dhsection;
+
+
+ &dhpackage;
+
+ comparison of a related protein to genomic DNA
+
+
+
+ &dhpackage;
+
+
+ options
+
+
+
+
+
+ protein-file dna-file
+
+
+
+
+
+ DESCRIPTION
+
+ not available
+
+
+
+ OPTIONS
+
+
+
+
+
+
+ Show summary of options.
+
+
+
+
+
+
+ Show version of program.
+
+
+
+
+
+ SEE ALSO
+
+ dba (1), dnal (1), estwise (1), estwisedb (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1).
+
+
+ AUTHOR
+
+ This manual page was written by &dhusername; &dhemail; for
+ the &debian; system (but may be used by others). Permission is
+ granted to copy, distribute and/or modify this document under
+ the terms of the &gnu; General Public License, Version 2 any
+ later version published by the Free Software Foundation.
+
+
+ On Debian systems, the complete text of the GNU General Public
+ License can be found in /usr/share/common-licenses/GPL.
+
+
+
+
+
+
+
+
--- wise-2.4.1.orig/debian/manpages.d/genewisedb.sgml
+++ wise-2.4.1/debian/manpages.d/genewisedb.sgml
@@ -0,0 +1,144 @@
+ manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+
+
+ Philipp">
+ Benner">
+
+ July 2006">
+
+ 1">
+ mail@philipp-benner.de">
+
+ GENEWISEDB">
+
+
+ Debian">
+ GNU">
+ GPL">
+]>
+
+
+
+
+ &dhemail;
+
+
+ &dhfirstname;
+ &dhsurname;
+
+
+ 2006
+ &dhusername;
+
+ &dhdate;
+
+
+ &dhucpackage;
+
+ &dhsection;
+
+
+ &dhpackage;
+
+ a database of proteins vs a database of genomic dna sequences
+
+
+
+ &dhpackage;
+
+
+ options
+
+
+
+
+
+ protein-input dna-input
+
+
+
+
+
+ DESCRIPTION
+
+ not available
+
+
+
+ OPTIONS
+
+
+
+
+
+
+ Show summary of options.
+
+
+
+
+
+
+ Show version of program.
+
+
+
+
+
+ SEE ALSO
+
+ dba (1), dnal (1), estwise (1), estwisedb (1), genewise (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1).
+
+
+ AUTHOR
+
+ This manual page was written by &dhusername; &dhemail; for
+ the &debian; system (but may be used by others). Permission is
+ granted to copy, distribute and/or modify this document under
+ the terms of the &gnu; General Public License, Version 2 any
+ later version published by the Free Software Foundation.
+
+
+ On Debian systems, the complete text of the GNU General Public
+ License can be found in /usr/share/common-licenses/GPL.
+
+
+
+
+
+
+
+
--- wise-2.4.1.orig/debian/manpages.d/dba.sgml
+++ wise-2.4.1/debian/manpages.d/dba.sgml
@@ -0,0 +1,155 @@
+ manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+
+
+ Philipp">
+ Benner">
+
+ July 2006">
+
+ 1">
+ mail@philipp-benner.de">
+
+ DBA">
+
+
+ Debian">
+ GNU">
+ GPL">
+]>
+
+
+
+
+ &dhemail;
+
+
+ &dhfirstname;
+ &dhsurname;
+
+
+ 2006
+ &dhusername;
+
+ &dhdate;
+
+
+ &dhucpackage;
+
+ &dhsection;
+
+
+ &dhpackage;
+
+ characterising shared regulatory regions of genomic DNA
+
+
+
+ &dhpackage;
+
+
+ options
+
+
+
+
+
+ seq1 seq2
+
+
+
+
+
+ DESCRIPTION
+
+ dba - standing for Dna Block Aligner, was developped by Niclas Jareborg,
+ Richard Durbin and Ewan Birney for characterising shared regulatory regions
+ of genomic DNA, either in upstream regions or introns of genes
+
+ The idea was that in these regions there would a series of shared motifs,
+ perhaps with one or two insertions or deletions but between motifs there
+ would be any length of sequence.
+
+ The subsquent model was a 3 state model which was log-odd'd ratio to a null
+ model of their being no examples of a motif in the two sequences.
+
+
+
+ OPTIONS
+
+
+
+
+
+
+
+ Show summary of options.
+
+
+
+
+
+
+
+ Show version of program.
+
+
+
+
+
+ SEE ALSO
+
+ dnal (1), estwise (1), estwisedb (1), genewise (1), genewisedb (1), genomewise (1), promoterwise (1), psw (1), pswdb (1), scanwise (1), scanwise_server (1).
+
+
+ AUTHOR
+
+ This manual page was written by &dhusername; &dhemail; for
+ the &debian; system (but may be used by others). Permission is
+ granted to copy, distribute and/or modify this document under
+ the terms of the &gnu; General Public License, Version 2 any
+ later version published by the Free Software Foundation.
+
+
+ On Debian systems, the complete text of the GNU General Public
+ License can be found in /usr/share/common-licenses/GPL.
+
+
+
+
+
+
+
+
--- wise-2.4.1.orig/debian/manpages.d/psw.sgml
+++ wise-2.4.1/debian/manpages.d/psw.sgml
@@ -0,0 +1,149 @@
+ manpage.1'. You may view
+ the manual page with: `docbook-to-man manpage.sgml | nroff -man |
+ less'. A typical entry in a Makefile or Makefile.am is:
+
+manpage.1: manpage.sgml
+ docbook-to-man $< > $@
+
+
+ The docbook-to-man binary is found in the docbook-to-man package.
+ Please remember that if you create the nroff version in one of the
+ debian/rules file targets (such as build), you will need to include
+ docbook-to-man in your Build-Depends control field.
+
+ -->
+
+
+
+ Philipp">
+ Benner">
+
+ July 2006">
+
+ 1">
+ mail@philipp-benner.de">
+
+ PSW">
+
+
+ Debian">
+ GNU">
+ GPL">
+]>
+
+
+
+
+ &dhemail;
+
+
+ &dhfirstname;
+ &dhsurname;
+
+
+ 2006
+ &dhusername;
+
+ &dhdate;
+
+
+ &dhucpackage;
+
+ &dhsection;
+
+
+ &dhpackage;
+
+ Protein Smith-Waterman and other comparisons
+
+
+
+ &dhpackage;
+
+
+ options
+
+
+
+
+
+ seq1 seq2
+
+
+
+
+
+ DESCRIPTION
+
+
+ psw is a short and sweet program for calculating smith waterman alginments
+ quickly. It was mainly written as C driver to test the underlying code which
+ is more useful in things like the Perl port.
+
+
+
+
+
+ OPTIONS
+
+
+
+
+
+
+ Show summary of options.
+
+
+
+
+
+
+ Show version of program.
+
+
+
+
+
+ SEE ALSO
+
+ dba (1), dnal (1), estwise (1), estwisedb (1), genewise (1), genewisedb (1), genomewise (1), promoterwise (1), pswdb (1), scanwise (1), scanwise_server (1).
+
+
+ AUTHOR
+
+ This manual page was written by &dhusername; &dhemail; for
+ the &debian; system (but may be used by others). Permission is
+ granted to copy, distribute and/or modify this document under
+ the terms of the &gnu; General Public License, Version 2 any
+ later version published by the Free Software Foundation.
+
+
+ On Debian systems, the complete text of the GNU General Public
+ License can be found in /usr/share/common-licenses/GPL.
+
+
+
+
+
+
+
+
--- wise-2.4.1.orig/debian/patches/04_wise2-pdflatex-update.dpatch
+++ wise-2.4.1/debian/patches/04_wise2-pdflatex-update.dpatch
@@ -0,0 +1,43 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 04_wise2-pdflatex-update.dpatch by Philipp Benner
+##
+## DP: Make wise2.tex pdflatex compatible.
+
+@DPATCH@
+
+diff -urNad wise-2.4.0~/docs/wise2.tex wise-2.4.0/docs/wise2.tex
+--- wise-2.4.0~/docs/wise2.tex 2007-08-06 10:25:05.000000000 +0200
++++ wise-2.4.0/docs/wise2.tex 2007-08-06 10:25:08.000000000 +0200
+@@ -1,6 +1,7 @@
+
+ \documentclass{article}
+-\usepackage{epsfig}
++%\usepackage{epsfig}
++\usepackage{graphicx}
+
+ \begin{document}
+ \newcommand{\programtext}[1]{{\tt #1}}
+@@ -707,8 +708,9 @@
+ \begin{figure}
+ \begin{center}
+ \leavevmode
+-\epsfxsize 300pt
+-\epsfbox{genewise21.eps}
++%\epsfxsize 300pt
++%\epsfbox{genewise21.eps}
++%\includegraphics[scale=0.75]{genewise21.pdf}
+ \newline
+ \caption{GeneWise21:93 Algorithm. The dark circles represent states, and the
+ arrows between them transitions. Black transitions are standard
+@@ -898,8 +900,9 @@
+ \begin{figure}
+ \begin{center}
+ \leavevmode
+-\epsfxsize 300pt
+-\epsfbox{genewise6.eps}
++%\epsfxsize 300pt
++%\epsfbox{genewise6.eps}
++%\includegraphics[scale=0.75]{genewise6.pdf}
+ \newline
+ \caption{GeneWise6:23}
+ \label{Figure:genewise623}
--- wise-2.4.1.orig/debian/patches/02_isnumber.dpatch
+++ wise-2.4.1/debian/patches/02_isnumber.dpatch
@@ -0,0 +1,18 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 02_isnumber.dpatch by Philipp Benner
+##
+## DP: Replace isnumber() (which does not exist on linux) by isdigit().
+
+@DPATCH@
+diff -urNad wise-2.4.0~/src/models/phasemodel.c wise-2.4.0/src/models/phasemodel.c
+--- wise-2.4.0~/src/models/phasemodel.c 2007-07-01 22:44:39.000000000 +0200
++++ wise-2.4.0/src/models/phasemodel.c 2007-07-16 00:24:16.000000000 +0200
+@@ -20,7 +20,7 @@
+ if( line[0] == '#' ) {
+ continue;
+ }
+- if( !isnumber(line[0]) ) {
++ if( !isdigit(line[0]) ) {
+ warn("Bad looking line in intron file, %s",line);
+ continue;
+ }
--- wise-2.4.1.orig/debian/patches/01_welcome-csh.dpatch
+++ wise-2.4.1/debian/patches/01_welcome-csh.dpatch
@@ -0,0 +1,28 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 01_welcome-csh.dpatch by Philipp Benner
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: No description.
+
+@DPATCH@
+diff -urNad wise-2.4.0~/src/makefile wise-2.4.0/src/makefile
+--- wise-2.4.0~/src/makefile 2007-07-15 23:39:24.000000000 +0200
++++ wise-2.4.0/src/makefile 2007-07-15 23:41:11.000000000 +0200
+@@ -109,7 +109,7 @@
+ bin :
+ mkdir bin
+ cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin
+- csh welcome.csh
++ ./welcome.csh
+
+ libs :
+ (cd base ; $(MAKE) CC="$(CC)" CFLAGS="$(CFLAGS)" libwisebase.a )
+diff -urNad wise-2.4.0~/src/welcome.csh wise-2.4.0/src/welcome.csh
+--- wise-2.4.0~/src/welcome.csh 2007-07-15 23:39:24.000000000 +0200
++++ wise-2.4.0/src/welcome.csh 2007-07-15 23:40:46.000000000 +0200
+@@ -1,4 +1,4 @@
+-#!/bin/tcsh -f
++#!/bin/sh
+
+ echo ""
+ echo "Welcome to Wise2.4"
--- wise-2.4.1.orig/debian/patches/00list
+++ wise-2.4.1/debian/patches/00list
@@ -0,0 +1,4 @@
+01_welcome-csh
+02_isnumber
+03_doc-nodycache
+04_wise2-pdflatex-update
--- wise-2.4.1.orig/debian/patches/03_doc-nodycache.dpatch
+++ wise-2.4.1/debian/patches/03_doc-nodycache.dpatch
@@ -0,0 +1,19 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 03_doc-nodycache.dpatch by Philipp Benner
+##
+## DP: Documentation bugfix.
+
+@DPATCH@
+diff -urNad wise-2.4.0~/docs/wise2.tex wise-2.4.0/docs/wise2.tex
+--- wise-2.4.0~/docs/wise2.tex 2003-03-26 12:47:08.000000000 +0100
++++ wise-2.4.0/docs/wise2.tex 2007-07-16 01:05:34.000000000 +0200
+@@ -1617,7 +1617,8 @@
+ \item[-hithelp] more detailed help on hitlist formats
+ \item[-dymem] memory style [default/linear/explicit]
+ \item[-kbyte] memory amount to use [4000]
+-\item[-\[no\]dycache] implicitly cache dy matrix usage (default yes)
++\item[-dycache] implicitly cache dy matrix usage (default)
++\item[-nodycache] do not implicitly cache dy matrix usage
+ \item[-dydebug] drop into dynamite dp matrix debugger
+ \item[-paldebug] print PackAln after debugger run if used
+ \item[-help] show help options
--- wise-2.4.1.orig/debian/dirs
+++ wise-2.4.1/debian/dirs
@@ -0,0 +1 @@
+usr/bin
--- wise-2.4.1.orig/debian/docs
+++ wise-2.4.1/debian/docs
@@ -0,0 +1 @@
+README
--- wise-2.4.1.orig/debian/control
+++ wise-2.4.1/debian/control
@@ -0,0 +1,68 @@
+Source: wise
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team
+Uploaders: Philipp Benner
+DM-Upload-Allowed: yes
+Build-Depends: debhelper (>= 5), dpatch (>= 2.0.21), texlive-latex-base,
+ texlive-extra-utils, hevea, docbook-to-man, libglib1.2-dev
+Standards-Version: 3.7.3
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/wise/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/wise/trunk/
+Homepage: http://www.ebi.ac.uk/~birney/wise2/
+
+Package: wise
+Architecture: any
+Depends: ${shlibs:Depends}
+Recommends: wise-doc (= ${source:Version})
+Description: comparison of biopolymers, commonly DNA and protein sequences
+ Wise2 is a package focused on comparisons of biopolymers, commonly DNA
+ and protein sequences. There are many other packages which do
+ this, probably the best known being BLAST package (from NCBI) and the
+ Fasta package (from Bill Pearson). There are other packages, such as
+ the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused
+ on hidden Markov models (HMMs) of biopolymers.
+ .
+ Wise2's particular forte is the comparison of DNA sequence at the level
+ of its protein translation. This comparison allows the simultaneous
+ prediction of say gene structure with homology based alignment.
+ .
+ Wise2 also contains other algorithms, such as the venerable Smith-Waterman
+ algorithm, or more modern ones such as Stephen Altschul's generalised
+ gap penalties, or even experimental ones developed in house, such as
+ dba. The development of these algorithms is due to the ease of developing
+ such algorithms in the enviroment used by Wise2.
+ .
+ Wise2 has also been written with an eye for reuse and maintainability.
+ Although it is a pure C package you can access its functionality
+ directly in Perl. Parts of the package (or the entire package) can
+ be used by other C or C++ programs without namespace clashes as all
+ externally linked variables have the unique identifier Wise2 prepended.
+
+Package: wise-doc
+Architecture: all
+Section: doc
+Recommends: wise (= ${source:Version}), xpdf-reader | pdf-viewer
+Description: documentation for the wise package
+ Wise2 is a package focused on comparisons of biopolymers, commonly DNA
+ and protein sequences. There are many other packages which do
+ this, probably the best known being BLAST package (from NCBI) and the
+ Fasta package (from Bill Pearson). There are other packages, such as
+ the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused
+ on hidden Markov models (HMMs) of biopolymers.
+ .
+ Wise2's particular forte is the comparison of DNA sequence at the level
+ of its protein translation. This comparison allows the simultaneous
+ prediction of say gene structure with homology based alignment.
+ .
+ Wise2 also contains other algorithms, such as the venerable Smith-Waterman
+ algorithm, or more modern ones such as Stephen Altschul's generalised
+ gap penalties, or even experimental ones developed in house, such as
+ dba. The development of these algorithms is due to the ease of developing
+ such algorithms in the enviroment used by Wise2.
+ .
+ Wise2 has also been written with an eye for reuse and maintainability.
+ Although it is a pure C package you can access its functionality
+ directly in Perl. Parts of the package (or the entire package) can
+ be used by other C or C++ programs without namespace clashes as all
+ externally linked variables have the unique identifier Wise2 prepended.
--- wise-2.4.1.orig/debian/wise-doc.doc-base.api
+++ wise-2.4.1/debian/wise-doc.doc-base.api
@@ -0,0 +1,12 @@
+Document: wise-api
+Title: Wise API Manual
+Author: Ewan Birney
+Abstract: This manual describes the wise api.
+Section: Science/Biology
+
+Format: PDF
+Files: /usr/share/doc/wise-doc/api.pdf.gz
+
+Format: HTML
+Index: /usr/share/doc/wise-doc/api/api.html
+Files: /usr/share/doc/wise-doc/api/*
--- wise-2.4.1.orig/debian/rules
+++ wise-2.4.1/debian/rules
@@ -0,0 +1,151 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+
+.NOTPARALLEL:
+include /usr/share/dpatch/dpatch.make
+
+configure: configure-stamp
+configure-stamp:
+ dh_testdir
+
+ touch configure-stamp
+
+build: patch build-stamp
+
+build-stamp: configure-stamp
+ dh_testdir
+
+ $(MAKE) -C src all
+ $(MAKE) -C debian/manpages.d
+
+# build documentation manually (docs/makefile is not useable)
+ cat src/models/*.tex src/dynlibsrc/*.tex | perl docs/gettex.pl > docs/temp.tex
+ cat docs/wise2api.tex docs/temp.tex docs/apiend.tex > docs/api.tex
+#
+ sed -i 's/ sw_wrap / sw\\_wrap /' docs/api.tex
+ sed -i 's/label{module_sequence\\_codon}/label{module_sequence_codon}/' docs/api.tex
+ sed -i 's/Wise2::GeneParameter21_wrap/Wise2::GeneParameter21\\_wrap/' docs/api.tex
+#
+ cd docs && pdflatex api.tex
+ cd docs && pdflatex api.tex
+ cd docs && pdflatex dynamite.tex
+ cd docs && pdflatex dynamite.tex
+# cd docs && ps2pdf genewise6.eps # segfaults on s390
+# cd docs && ps2pdf genewise21.eps
+ cd docs && pdflatex wise2.tex
+ cd docs && pdflatex wise2.tex
+
+ cd docs && hevea api.tex
+ cd docs && hevea api.tex
+ cd docs && hevea dynamite.tex
+ cd docs && hevea dynamite.tex
+ cd docs && hevea wise2.tex
+ cd docs && hevea wise2.tex
+
+ mkdir -p docs/api
+ mkdir -p docs/dynamite
+ mkdir -p docs/wise2
+
+ mv docs/api.html docs/api
+ mv docs/dynamite.html docs/dynamite
+ mv docs/wise2.html docs/wise2
+
+ touch $@
+
+clean: unpatch
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp configure-stamp
+
+ $(MAKE) -C src clean
+ $(MAKE) -C debian/manpages.d clean
+
+# bugfix
+ $(RM) -r src/oldbin
+ $(RM) src/models/{dba,psw,dnal,genomewise,pswdb,scanwise,estwise,genewise,sywise,genewisedb,promoterwise,pseudowise,estwisedb}
+ $(RM) src/network/scanwise_server
+
+# clean documentation
+ $(RM) docs/temp.tex
+ $(RM) docs/api.*
+ $(RM) docs/wise2.image.tex
+ $(RM) docs/*.pdf
+ $(RM) docs/*.aux
+ $(RM) docs/*.log
+ $(RM) docs/*.toc
+ $(RM) docs/*.pdf
+ $(RM) docs/*.dvi
+ $(RM) docs/*.ps
+ $(RM) docs/*.4ct
+ $(RM) docs/*.4tc
+ $(RM) docs/*.css
+ $(RM) docs/*.idv
+ $(RM) docs/*.lg
+ $(RM) docs/*.tmp
+ $(RM) docs/*.xref
+ $(RM) docs/*.haux
+ $(RM) docs/*.htoc
+ $(RM) docs/*.html
+
+ $(RM) -r docs/api
+ $(RM) -r docs/dynamite
+ $(RM) -r docs/wise2
+
+ dh_clean
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+
+# $(MAKE) install DESTDIR=$(CURDIR)/debian/wise
+ install -m 755 src/bin/* debian/wise/usr/bin
+ install -m 755 src/models/genomewise debian/wise/usr/bin
+
+binary-indep: build install
+ dh_testdir -i
+ dh_testroot -i
+ dh_installchangelogs -i
+ dh_installdocs -i
+ dh_installexamples -i
+ dh_installman -i
+ dh_link -i
+ dh_strip -i
+ dh_compress -i
+ dh_fixperms -i
+ dh_installdeb -i
+ dh_gencontrol -i
+ dh_md5sums -i
+ dh_builddeb -i
+
+binary-arch: build install
+ dh_testdir -a
+ dh_testroot -a
+ dh_installchangelogs -a
+ dh_installdocs -a
+ dh_installexamples -a
+ dh_installman -a
+ dh_link -a
+ dh_strip -a
+ dh_compress -a
+ dh_fixperms -a
+ dh_installdeb -a
+ dh_shlibdeps -a
+ dh_gencontrol -a
+ dh_md5sums -a
+ dh_builddeb -a
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install configure
--- wise-2.4.1.orig/debian/watch
+++ wise-2.4.1/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+http://www.ebi.ac.uk/~birney/wise2/ (?:./)?wise(.*)\.tar\.gz \
+ debian uupdate
--- wise-2.4.1.orig/debian/wise-doc.doc-base.dynamite
+++ wise-2.4.1/debian/wise-doc.doc-base.dynamite
@@ -0,0 +1,13 @@
+Document: wise-dynamite
+Title: Wise dynamite Manual
+Author: Ewan Birney
+Abstract: This manual describes the dynamite code generating
+ language for dynamic programming.
+Section: Science/Biology
+
+Format: PDF
+Files: /usr/share/doc/wise-doc/dynamite.pdf.gz
+
+Format: HTML
+Index: /usr/share/doc/wise-doc/dynamite/dynamite.html
+Files: /usr/share/doc/wise-doc/dynamite/*
--- wise-2.4.1.orig/debian/wise-doc.doc-base.wise
+++ wise-2.4.1/debian/wise-doc.doc-base.wise
@@ -0,0 +1,12 @@
+Document: wise
+Title: Debian wise2 Manual
+Author: Ewan Birney, Richard Copley
+Abstract: This manual describes wise program usages.
+Section: Science/Biology
+
+Format: PDF
+Files: /usr/share/doc/wise-doc/wise2.pdf.gz
+
+Format: HTML
+Index: /usr/share/doc/wise-doc/wise2/wise2.html
+Files: /usr/share/doc/wise-doc/wise2/*
--- wise-2.4.1.orig/debian/changelog
+++ wise-2.4.1/debian/changelog
@@ -0,0 +1,92 @@
+wise (2.4.1-4) unstable; urgency=low
+
+ * Changed the doc-base section according to the new policy
+ [Charles Plessy].
+
+ -- Philipp Benner Mon, 31 Mar 2008 10:07:35 +0200
+
+wise (2.4.1-3) unstable; urgency=low
+
+ * New maintainer e-mail address.
+ * debian/control: Added DM-Upload-Allowed: yes.
+
+ -- Philipp Benner Mon, 14 Jan 2008 18:33:27 +0100
+
+wise (2.4.1-2) unstable; urgency=low
+
+ * Using official Vcs-Browser and Vcs-Svn fields (debian/control).
+ * Moved the Homepage: field out from the package's description
+ + (Charles Plessy).
+ * Converted copyright file to machine interpretable format.
+ * Changed maintainer to Debian-Med Packaging Team.
+
+ -- Philipp Benner Sun, 02 Dec 2007 16:15:50 +0100
+
+wise (2.4.1-1) unstable; urgency=low
+
+ * New upstream release.
+
+ -- Philipp Benner Sat, 15 Sep 2007 17:18:49 +0200
+
+wise (2.4.0-3) unstable; urgency=low
+
+ * Removed debtags from debian/control.
+ * Updated package description (Closes: #435904).
+ * Excluded genewise21.eps and genewise6.eps from documentation
+ + (workaround for a bug in gs-esp).
+
+ -- Philipp Benner Sun, 05 Aug 2007 20:21:35 +0200
+
+wise (2.4.0-2) unstable; urgency=low
+
+ * Converted wise2.tex to a pdflatex compatible latex file
+ + (workaround for a bug in dvips)
+
+ -- Philipp Benner Fri, 27 Jul 2007 18:46:33 +0200
+
+wise (2.4.0-1) unstable; urgency=low
+
+ * New upstream release (Closes: #431392)
+ * New dpatch (02_isnumber): src/models/phasemodel.c: replaces isnumber() by isdigit()
+ * New dpatch (03_doc-nodycache): docs/wise2.tex: minor bugfix
+
+ -- Philipp Benner Tue, 24 Jul 2007 11:58:36 +0200
+
+wise (2.2.0-5) unstable; urgency=low
+
+ * Removed obsolete dependencies (Closes: #422123)
+
+ -- Philipp Benner Sun, 6 May 2007 22:42:27 +0200
+
+wise (2.2.0-4) unstable; urgency=low
+
+ * Adapted debian-med tags
+ * Uscan support
+ * Migrating to texlive
+ * use /bin/sh instead of /bin/csh in src/welcome.csh
+
+ -- Philipp Benner Tue, 27 Mar 2007 19:29:08 +0200
+
+wise (2.2.0-3) unstable; urgency=low
+
+ * package tags
+ * fixed typos in package description
+
+ -- Philipp Benner Thu, 21 Sep 2006 14:22:39 +0200
+
+wise (2.2.0-2) unstable; urgency=low
+
+ * removed \ref tags from package description
+ * moved examples to package wise-doc
+ * fixed typo in README.Debian
+ * minor changes in debian/control
+ * fixed typo in package description (Closes: #380451)
+ * new html documentation
+
+ -- Philipp Benner Sun, 30 Jul 2006 14:08:20 +0200
+
+wise (2.2.0-1) unstable; urgency=low
+
+ * Initial release (Closes: #379604)
+
+ -- Philipp Benner Sun, 23 Jul 2006 17:29:49 +0200
--- wise-2.4.1.orig/debian/manpages
+++ wise-2.4.1/debian/manpages
@@ -0,0 +1,12 @@
+debian/manpages.d/dba.1
+debian/manpages.d/dnal.1
+debian/manpages.d/estwise.1
+debian/manpages.d/estwisedb.1
+debian/manpages.d/genewise.1
+debian/manpages.d/genewisedb.1
+debian/manpages.d/genomewise.1
+debian/manpages.d/promoterwise.1
+debian/manpages.d/psw.1
+debian/manpages.d/pswdb.1
+debian/manpages.d/scanwise.1
+debian/manpages.d/scanwise_server.1
--- wise-2.4.1.orig/debian/compat
+++ wise-2.4.1/debian/compat
@@ -0,0 +1 @@
+5
--- wise-2.4.1.orig/debian/wise-doc.docs
+++ wise-2.4.1/debian/wise-doc.docs
@@ -0,0 +1,6 @@
+docs/api.pdf
+docs/dynamite.pdf
+docs/wise2.pdf
+docs/api
+docs/dynamite
+docs/wise2
--- wise-2.4.1.orig/debian/README.Debian
+++ wise-2.4.1/debian/README.Debian
@@ -0,0 +1,7 @@
+wise for Debian
+--------------------------------------------------------------------------------
+
+You may want to copy /usr/share/doc/wise-doc/examles/* (distributed by wise-doc)
+to your home directory and set WISECONFIGDIR appropriately.
+
+ -- Philipp Benner , Mon, 14 Jan 2008 18:36:28 +0100
--- wise-2.4.1.orig/debian/wise-doc.examples
+++ wise-2.4.1/debian/wise-doc.examples
@@ -0,0 +1 @@
+wisecfg/*
--- wise-2.4.1.orig/debian/copyright
+++ wise-2.4.1/debian/copyright
@@ -0,0 +1,68 @@
+This package was downloaded from http://www.ebi.ac.uk/~birney/wise2/
+
+Files: *
+Copyright: © 1996-2001 Genome Research Limited (GRL) and
+ Ewan Birney and Sean Eddy
+License: Other
+ All of the documentation and software included in the dyc directory of the
+ Wise2 package directory is copyrighted by Genome Research Limited
+ (GRL) and other individuals where appropriate. This license is modelled
+ after the 'BSD' style license and is appropriate for use by both
+ academic and commercial sites, without placing any restriction on the
+ distribution of source code from other sources with this software.
+ .
+ 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.Neither the name GRL nor the names of its contributors may be used
+ to endorse or promote products derived from this software without
+ specific prior written permission.
+ .
+ It is considered polite to indicate where appropriate that software which
+ is developed using this source code includes a statement that it was developed
+ using the Wise2 soure code. This is not a requirement however.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE GRL 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 GRL 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.
+
+Files: src/HMMer2/*
+Copyright: © 1992-1996 Sean R. Eddy
+License: GPL-2
+ This source code is distributed under the terms of the
+ GNU General Public License. See the files COPYING and
+ GNULICENSE for details.
+
+Files:
+ src/dynlibsrc/histogram.dy, src/dynlibsrc/histogram.pod,
+ src/dynlibsrc/histogram.tex
+Copyright: © 1996-1999 Genome Research Limited (GRL) and Sean Eddy
+License: LGPL-any
+
+Files: debian/*
+Copyright: © 2006-2007 Philipp Benner
+License: GPL-2+
+ The Debian packaging information is under the GPL, version 2 or later.
+ This package was debianized by Philipp Benner on Sun, 23 Jul 2006.
+
+On Debian GNU/Linux systems, the complete text of the GNU General
+Public License can be found in `/usr/share/common-licenses/GPL' and the
+complete text of the GNU Lesser General Public License can be found in
+`/usr/share/common-licenses/LGPL'.