debian/ 0000755 0000000 0000000 00000000000 12217720236 007170 5 ustar debian/boxshade.1.xml 0000644 0000000 0000000 00000067133 12105353320 011650 0 ustar
Steffen">
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&dhtitle;&dhpackage;&dhrelease;&dhdate;KayHofmannISRECBioinformatics GroupCH-1066Epalinges s/LausanneSwitzerlandWrote Boxshade.kay.hofmann@memorec.comMichaelDBaronBBSRC Institute for Animal HealthPirbright,
SurreyGU24 0NFU.K.Wrote Boxshade.michael.baron@bbsrc.ac.ukHarmutSchirmerTechnische FakultaetKaiserstr. 2D-24143KielGermany
C port of Boxshade. (don't send Kay or Michael any questions concerning the 'C' version of boxshade)
hsc@techfak.uni-kiel.de
&dhfirstname;
&dhsurname;
Wrote the manpage.
&dhemail;
CharlesPlessy
Updated the manpage
plessy@debian.org
1997Kay Hofmann, Michael Baron and Harmut Schirmer20032007&dhusername;Charles Plessy
The above copyright notices refer to the program and its manpage respectively.
BOXSHADE is completely public-domain and may be passed around and modified without any notice to the authors.
This manual page was written for the &debian; system but may be used by others. Permission is granted to copy, distribute and/or modify this document under same terms as &dhpackage; itself.
&dhucpackage;
&dhsection;
&dhpackage;Pretty-printing of multiple sequence alignments&dhpackage;DESCRIPTIONBOXSHADE is a program for pretty-printing multiple alignment output. The program itself doesn't do any alignment, you have to use a multiple alignment program like ClustalW or Pileup and use the output of these programs as input for BOXSHADE.
Show the help.
Show the help and extend command line.
Use defaults, no unnecessary questions.
Use default numbering.
Assume DNA sequences, use box_dna.par.
Create separate files for multiple pages.
Shading according to sequence No. xxx.
xxxxx is input file name.
xxxxx is output file name.
xxxxx is parameter file name.
xxxxx is file name for similar residues def.
xxxxx is file name for grouping residues def.
x is the fraction of sequences that must agree for a consensus.
x is output device class (see below).
x is input file format (see below).
Print ruler line.
Create consensus line.
xyz are consensus symbols.
If the one above does not work, try this one.
Output files lines are terminated with LF only.
Output files lines are terminated with CR only.
Output files lines are terminated with CRLF.
This manual page was written for the &debian; distribution
because the original program does not have a manual page. The presented information comes from the documentation of the Web Service of the 3.21 version that is not available as a Debian package.
BOXSHADE is a program for creating good looking printouts from
multiple-aligned protein or DNA sequences. The program does no alignment
by itself, it has to take as input a file preprocessed by a multiple
alignment program or a multiple file editor. See below for a list of
supported input formats and output devices. In the standard BOXSHADE
output, identical and similar residues in the multiple-alignment chart
are represented by different colors or shadings. There are some more
options concerning the kind of shading to be applied, sequence numbering,
consensus output and so on. The user interface is a bit clumsy at
the moment, one has to answer a lot of questions in order to get the
desired output. There is, however, the possibility to use default
parameters from a standard parameter file or to supply the program
with parameters from the command line. At the moment, the VMS and DOS
versions of BOXSHADE have identical user interfaces.
Input formats
BOXSHADE 3.2 knows about the following input file formats: (some of
the are generally used only for MSDOS or VMS systems) + CLUSTAL and
CLUSTALV, multiple alignment program, DOS/VMS/MAC default extension .ALN
+ ESEE, multiple sequence editor, DOS default extension .ESE + PHYLIP,
phylogenetic analysis package, DOS, VMS, UNIX default extension .PHY +
PILEUP and PRETTY of the GCG sequence analysis package VMS/UNIX default
extensions .MSF and .PRE NB!! you are strongly encouraged NOT to use the
PRETTY format as input, it may be incompatible with the revised version
of .MSF input. We can't actually think why anyone would use this format
now, .MSF files are more useful generally. + MALIGNED, multiple sequence
editor, VMS only default extension .MAL BOXSHADE tries to determine the
file type from the extension but will work also if different extensions
are used.
Output devicesPOSTSCRIPT/EPS creates POSTSCRIPT(TM) files for printing on
a Laserprinter or for further conversion with a POSTSCRIPT interpreter
(like GHOSTSCRIPT) + HPGL for export to various graphics programs or
for conversion/printing with the shareware program PRINTGL. Plotting
BOXSHADE output on a plotter is generally not recommended + RTF for
export to various word-processing and graphics programs + CRT, uses direct
screen writes to the PC-monitor. Possible options depend on the graphics
adapter used. This output device is supported only in the MSDOS version. +
ANSI. On a PC, this option uses an ANSI device driver (ANSI.SYS) that has
to be loaded in CONFIG.SYS previously. Possible character renditions are
reverse, bold,underlined, blinking etc. On non-DOS systems, this option
behaves more or less like the VT100 output mode. + VT100 for display on a
VT100 compatible terminal or emulator. + ReGISterm for display on a ReGIS
compatible graphics terminal or emulator. + ReGISfile for later conversion
by the program RETOS (copyright DEC) in order to print on DIGITALs
printer series. + LJ250 for printing on DIGITALS LJ250 color printer. +
ASCII output showing either the conserved residues or the varying ones
(others as '-'). + FIG file for xfig 2.1. + PICT files for import to Mac
and PC graphics progs. Some of the formats above offer the possibility
of scaling the characters and of rotating the plot. Character size has
to be entered in 'point' units. Normal output orientation is in portrait
mode (PS/EPS/HPGL/PICT only), to obtain output in landscape orientation,
'rotate plot = y' has to be chosen. When creating multi-page output,
all pages are contained in a single output file. If one page per file
is desired, one has to use the command line parameter /SPLIT. This is
enforced when requesting EPSF or PICT file output, as multi-page EPSFs
are a contradiction of the purpose of an EPSF and large PICT files would
probably be too big for most personal computers. While using the terminal
as output device, the 'RETURN' key has to be pressed to obtain the next
page of output.
Sequence numberingStarting with version 2.2 there
is the possibility to add numbering to the output files. The numbers are
printed between the sequence names and the sequence itself. Since most of
the input-files either use no numbering or number the first position in
the alignment always with a "1" (and that does not necessarily reflect
the numbers within the original sequence), the user is asked to enter
the starting position for each sequence. The command line flag /DEFNUM
suppressed that question, a starting position of 1 is assumed for all
sequences. Boxshade starts with the value entered for the leftmost
position and continues numbering every valid symbol, skipping blanks,
'-','.' and stuff like that.
Default parametersSeveral people using
previous releases of BOXSHADE pointed me to the need of having default
parameters for the various questions asked by the program. They argued
that most sites only use one type of input files, one output device and
one choice of colors for the output. I therefore added a management of
default parameters allowing two levels of assistance to the user. 1) all
default parameters are contained in an ASCII file that can be modified
easily to accommodate the users taste. The format is roughly documented
within the file-header, it resembles the keyboard input one has to make
if using the program interactively. There are two such files supplied
with this release of BOXSHADE, BOX_DNA.PAR and BOX_PEP.PAR , holding
some example parameters for peptide and dna-comparisons. there are no
big differences between these two, the major one is that when shading
DNA-comparisons one doesn't care of "similar" residues. 2) to run the
program with minimal user interaction, I have added the possibility to
use command line parameters. At the moment, you can use: /check : list
all allowed command line parameters (this list) and allows parameters to
be added. /def : program runs without questions, BOX_PEP.PAR is used as
default /dna : makes the program use BOX_DNA.PAR as parameter file /pep :
makes the program use BOX_PEP.PAR as parameter file /in=xxx : makes the
program take xxx as input file /out=yyy : makes the program take yyy as
output file (note1) /par=zzz : makes the program use zzz as a default
parameter file /type=1 : makes the program assume an input file of type
1 (PRETTY/MSF) /dev=1 : makes the program assume and output device of
type 1 (CRT) /numdef : use default numbering (all sequences starting
with "1") /thr : threshold fraction of residues that must agree for a
consensus /split : forces one page per file output, creates multiple
output files. /cons : makes the program create an additional consensus
line (see below) /symbcons=: influences the way the consensus line is
displayed. (see below) /unix : writes output files in unix style (LF only)
(note2) /dos : writes output files in DOS style (CR/LF) (note2) note1:
on unix machines, use out=OUTPUT for terminal output on DOS machines,
use out=con: on VMS machines, use out=tt: note2: if no mode is specified,
the native style of the machine is used.
ATTENTIONon unix systems, the dash (-) instead of the slash (/) has to be used as separation character for command line parameters. For example, a valid unix command line is: boxshade -def -numdef -cons -symbcons=" .*"Shading strategies (similarity to consensus or single sequence)
Starting with version 3, BOXSHADE has a new shading system. The first
difference is the introduction of a threshold fraction of residues that
must agree for there to be a consensus. Previously, the program assumed
that SOME residue was always the consensus. If no two residues were the
same, the first sequence provided the consensus residue. This threshold
fraction can be any number between 0.0 and 1.0. The number of sequences
that must agree for there to be a consensus is, as you might expect,
this fraction times the total number of sequences in the alignment
(fractions of a sequence count as one, e.g. 3.2 becomes 4). The second
difference is the idea of 'consensus by similarity'; this tries to take
account of the situations where all the sequences may have (for example)
R or K at a position, but neither in a majority. It would not be logical
to shade one type of residue as 'identical' and the other as 'similar';
the threshold function might also eliminate both as being in too small
numbers. Therefore, if there is not a single residue that is conserved
(greater than the threshold) at a position, the program looks for a
'group' of amino acids that fulfills the requirements. 'Groups' are
defined in the .grp files. Users can tailor these to their personal
prejudices. Any amino acid not listed is assumed not to be in a group. All
members of a group are considered to be mutually similar, unlike the
.sim files, described below. If consensus by similarity is found, all the
residues in the consensus are shaded using the 'similar' shading defined
by the user. If the user does not select 'shading by similarity', only
identity-type consensus is looked at. If an identity-type consensus is
found, and similarity shading is in operation, the program looks to see
if the remaining residues are similar to the consensus residue. Here the
box_xxx.sim files are used. The main difference between relationships
in these files and those in the .grp files is that, e.g. in a .grp
file the line STA means that all three a.a.s are mutually similar. In
a .sim file S TA means that both T and A are considered similar to S,
where there is a conserved S residue in more than threshold number of
sequences. However, it does NOT mean that T and A are similar to each
other. Note that cases where two residues, or groups of residues,
fulfill the threshold requirements (as could happen with values of
the thr. fraction less than or equal to 0.5) are treated as having no
consensus. This describes the main shading model 'shading according to
a consensus'. The alternative model is called 'shading according to
a master sequence'. In this case the user is prompted for a sequence
of the alignment and consecutively that sequence is taken to be the
'consensus'. Only those residues become shaded that are identical or
similar to the chosen sequence. Output obtained with this option tends
to be less shaded and neglects similarities between the other (non-chosen)
sequences. Starting in V2.7, this 'master sequence' can be hidden. Thus,
it only influences the shading of the other sequences without being
shown itself.
Consensus displayStarting with version 2.5, BOXSHADE
offers the possibility to create an additional line holding a consensus
symbol. This line can either be obtained by using the command line
qualifier /CONS or interactively by answering the question ' create
consensus? '. The way this consensus line is displayed can be modified
by the command line parameter SYMBCONS=xyz, by editing the respective
entry in the .PAR file or interactively. Since the SYMBCONS syntax is
not intuitive, here a brief description: The SYMBCONS parameter consist
of exactly three symbols: + the first one stands for 'normal' sequence
residues that are not involved in any similar/identical relationship. +
the second symbol represents positions that are similar in all sequences
of the alignment. See the files BOX_PEP.SIM and BOX_DNA.SIM to see
what residues are considered similar. + the third symbol represents
positions that are identical in all sequences of the alignment. A
SYMBCONS parameter string " .*" (blank/point/asterisk) means: label
all positions in the alignment with totally identical residues by an
asterisk, all positions with all similar residues by a point and do not
mark the other positions. The letter 'B' can be used instead of the blank,
this is necessary e.g. when using the command line option /SYMBCONS=B.*
which gives the same result as the above example. The option /SYMBCONS=
.* would result in an unexpected behaviour because MSDOS squeezes blanks
out of the command line. Besides points, asterisks and other symbols,
there are two special characters when they appear in the SYMBCONS string:
'L' and 'U'. An 'L' means, that a lowercase representation of the
most abundant residue at that position is to be used instead of a fixed
consensus symbol while an 'U' means an uppercase character representation
of that residue. A possible application would be the SYMBCONS string "
LU" where similar residues are represented by lowercase characters and
identical by uppercase characters.
Shareware/PD programs useful in conjunction with BOXSHADE
multiple alignment files that to be used by BOXSHADE can be created,
amongst others, by the following PD/freeware programs: + PHYLIP by Joe
Felsenstein, available by ftp from anthro.utah.edu + ESEE by Eric Cabot,
available from the same sources as BOXSHADE (see above) + CLUSTAL by Des
Higgins, ditto for preview/conversion of POSTSCRIPT files, the program
GHOSTSCRIPT from GNU software foundation is highly recommended. It is
available from all major MSDOS ftp-sites (e.g. SIMTEL or ftp.uni-koeln.de)
There is also a version tested for use with boxshade available at
vax0.biomed.uni-koeln.de although this might be not the most recent
release. for Mac users, there is MacGhostscript, also available from the
main archives (info-mac, umich and their mirrors). A *very* good tool
for putting a preview image into an EPSF file, often a prerequisite for
incorporating into a drawing package, is PS2EPS, by Peter Lerup. This can
be found on info-mac. for preview/conversion of HPGL files, the shareware
program PRINTGL 1.18 by Cary Ravitz is highly recommended. It is available
from many MSDOS ftp sites and from netserv@embl-heidelberg.de - output on
dot printers - Since PRINTGL offers a broad choice of printer types and
is a nice program, I recommend its use for printing BOXSHADE output on
non-POSTSCRIPT printers. Use HPGL output with options 0F1N for normal
residues 2F1N for identical residues 3F1N for similar residues 2F4N
for conserved residues 8 for character size not rotated (these are the
standard parameters in BOX_PEP.PAR) for creating a HPGL files. (lets call
it TEST.PLT) Now use PRINTGL either interactively by calling PMI or use
a command line like: PRINTGL /Fx/S0340/Waaac/Ptest.plt where test.plt is
to be replaced by the filename to convert and the x in the expression
/Fx is to be replaced by the letter of the printer you use. (See the
PRINTGL documentation for further details)
RESTRICTIONS
The RTF output and PHYLIP input implementations are still
experimental. Please tell me of your experiences with the program. +
the current DOS version supports only 13 sequences with 2000 residues
each. This parameters can be easily changed in the source code. If you
cannot compile the sources because you are lacking a pascal compiler,
contact the author for precompiled versions
CITING BOXSHADE
There is no publication on BOXSHADE and none is planned. Most people just use it for figures in publications and don't mention anything, this is ok for the authors of BOXSHADE. If you really feel like mentioning BOXSHADE, you could either acknowledge it in the figure legend or in the Mat&Meth part on sequence analysis.
SEE ALSO/etc/boxshade/*.parseaview1kalign1
debian/rules 0000755 0000000 0000000 00000000656 12105356665 010266 0 ustar #!/usr/bin/make -f
# -*- makefile -*-
# debian/rules for boxshade
# Andreas Tille , GPL
export DH_VERBOSE=1
%:
dh $@
override_dh_auto_build:
$(MAKE) -f makefile.unx CFLAGS="$(shell dpkg-buildflags --get CFLAGS)" CPPFLAGS="$(shell dpkg-buildflags --get CPPFLAGS)" LDFLAGS="$(shell dpkg-buildflags --get LDFLAGS)"
override_dh_clean:
rm -f boxshade *.o
dh_clean
get-orig-source:
sh debian/get-orig-source
debian/patches/ 0000755 0000000 0000000 00000000000 12217720236 010617 5 ustar debian/patches/kickOutGets.patch 0000644 0000000 0000000 00000013363 11054126367 014105 0 ustar --- boxshade-3.3.1.orig/box.c
+++ boxshade-3.3.1/box.c
@@ -136,6 +136,7 @@
----------------------------------------------------------------------- */
+#include
#define BX_TYPES_G
#include "bx_types.h"
@@ -193,7 +194,7 @@
if (cl != NULL) {
printf("actual command line: %s\n", cl);
printf("add to command line: ");
- Gets(ncl);
+ Gets(ncl,sizeof(ncl)-1);
} else
*ncl = '\0';
return ncl;
@@ -389,7 +390,7 @@
if (explain == NULL) return FALSE;
for (;;) {
printf("%s %s does not exist, enter filename: ", explain, neu);
- Gets(fn);
+ Gets(fn,sizeof(fn)-1);
if (fexist(fn)) return TRUE;
strcpy(neu, fn);
printf("\007file does not exist \n");
@@ -413,7 +414,7 @@
do {
printf("Default-parameter file %s does not exist, enter filename: ",
parname);
- Gets(parname);
+ Gets(parname,sizeof(parname)-1);
ok = fexist(parname);
if (!ok)
printf("\007file does not exist \n");
@@ -523,13 +524,15 @@
do {
if (!clinflag) {
printf("name of aligned input-file : ");
- Gets(inname);
+ Gets(inname,sizeof(inname)-1);
printf("\n");
}
ok = fexist(inname);
if (!ok) {
- printf("\007aligned input file does not exist \n");
- clinflag = FALSE;
+ fprintf(stderr,"\007aligned input file '%s' could not be read: %s, maxsize of name is %d.\n",inname,strerror(errno),sizeof(inname));
+ if (clinflag) {
+ exit(-1);
+ }
}
} while (!ok);
/**** ask for infile type ****/
@@ -778,7 +781,7 @@
ok = FALSE;
do {
printf("Similarity-file %s does not exist, enter filename: ", simname);
- Gets(simname);
+ Gets(simname,sizeof(simname)-1);
ok = fexist(simname);
if (!ok)
printf("\007file does not exist \n");
@@ -792,7 +795,7 @@
ok = FALSE;
do {
printf("Group-file %s does not exist, enter filename: ", grpname);
- Gets(grpname);
+ Gets(grpname,sizeof(grpname)-1);
ok = fexist(grpname);
if (!ok)
printf("\007file does not exist \n");
@@ -851,7 +854,7 @@
/**** ask for matrix file ****/
*instring = '\0';
printf("name of matrix output-file : ");
- Gets(identname);
+ Gets(identname,sizeof(identname)-1);
printf("\n");
}
--- boxshade-3.3.1.orig/bx_read.c
+++ boxshade-3.3.1/bx_read.c
@@ -2,9 +2,9 @@
FILE *infile = NULL;
-char *Gets(char *s) {
+char *Gets(char *s, size_t length) {
fflush(stdout);
- return gets(s);
+ return fgets(s,length,stdin);
}
/*
@@ -23,7 +23,7 @@
BOOL cr, eoln = FALSE;
if (f == stdin)
- return Gets(l);
+ return Gets(l,sze-1);
if (feof(f)) return NULL;
--- boxshade-3.3.1.orig/bx_read.h
+++ boxshade-3.3.1/bx_read.h
@@ -4,7 +4,7 @@
#include "bx_types.h"
-extern char *Gets(char *s);
+extern char *Gets(char *s, size_t length);
extern char *Fgets(char *l, size_t sze, FILE *f);
extern void read_file_clustal(void);
--- boxshade-3.3.1.orig/dv_ansi.c
+++ boxshade-3.3.1/dv_ansi.c
@@ -79,7 +79,7 @@
lc[4] = FALSE;
if (!cloutflag) {
printf("filename for %s-output (return for terminal) : ", term);
- gets(outname);
+ Gets(outname,sizeof(outname)-1);
}
}
--- boxshade-3.3.1.orig/dv_ascii.c
+++ boxshade-3.3.1/dv_ascii.c
@@ -71,7 +71,7 @@
lc[4] = FALSE;
if (!cloutflag) {
printf("filename for ASCII-output (return for terminal) : ");
- gets(outname);
+ Gets(outname,sizeof(outname)-1);
}
}
--- boxshade-3.3.1.orig/dv_fig.c
+++ boxshade-3.3.1/dv_fig.c
@@ -154,7 +154,7 @@
}
if (!cloutflag) {
printf("name of fig-file : ");
- gets(outname);
+ Gets(outname,sizeof(outname)-1);
}
}
--- boxshade-3.3.1.orig/dv_hpgl.c
+++ boxshade-3.3.1/dv_hpgl.c
@@ -268,7 +268,7 @@
}
if (!cloutflag) {
printf("filename for HPGL-output : ");
- gets(outname);
+ Gets(outname,sizeof(outname)-1);
}
}
--- boxshade-3.3.1.orig/dv_html.c
+++ boxshade-3.3.1/dv_html.c
@@ -158,7 +158,7 @@
if (!cloutflag)
do {
printf("filename for HTML-output : ");
- gets(outname);
+ Gets(outname,sizeof(outname)-1);
} while (*outname == '\0');
}
--- boxshade-3.3.1.orig/dv_lj250.c
+++ boxshade-3.3.1/dv_lj250.c
@@ -81,7 +81,7 @@
lc[4] = FALSE;
if (!cloutflag) {
printf("name of print-file : ");
- gets(outname);
+ Gets(outname,sizeof(outname)-1);
}
}
--- boxshade-3.3.1.orig/dv_pict.c
+++ boxshade-3.3.1/dv_pict.c
@@ -201,7 +201,7 @@
}
if (!cloutflag) {
printf("filename for PICT file output : ");
- gets(outname);
+ Gets(outname,sizeof(outname)-1);
}
}
--- boxshade-3.3.1.orig/dv_ps.c
+++ boxshade-3.3.1/dv_ps.c
@@ -199,7 +199,7 @@
if (!cloutflag)
do {
printf("filename for POSTSCRIPT-output : ");
- gets(outname);
+ Gets(outname,sizeof(outname)-1);
} while (*outname == '\0');
}
--- boxshade-3.3.1.orig/dv_regis.c
+++ boxshade-3.3.1/dv_regis.c
@@ -126,7 +126,7 @@
lc[4] = FALSE;
if (!cloutflag) {
printf("filename for REGIS-output : ");
- gets(outname);
+ Gets(outname,sizeof(outname)-1);
}
}
--- boxshade-3.3.1.orig/dv_rtf.c
+++ boxshade-3.3.1/dv_rtf.c
@@ -127,7 +127,7 @@
}
if (!cloutflag) {
printf("filename for RTF-output : ");
- gets(outname);
+ Gets(outname,sizeof(outname)-1);
}
}
--- boxshade-3.3.1.orig/bx_misc.c
+++ boxshade-3.3.1/bx_misc.c
@@ -60,14 +60,22 @@
BOOL fexist(char *fname)
{
- BOOL Result;
FILE *f;
+ if (NULL == fname) {
+ fprintf(stderr,"fexist: serious programming error, the filename is NULL.\n");
+ exit(-1);
+ }
+
f = fopen(fname, TXT_RD);
- Result = (f != NULL);
- if (f != NULL)
+ if (f) {
fclose(f);
- return Result;
+ return TRUE;
+ }
+ else {
+ // leaving it to calling function to interpret errno.
+ return FALSE;
+ }
}
int indx(char *mainstring, char *substring)
debian/patches/remove-newlines.patch 0000644 0000000 0000000 00000001072 12105332416 014752 0 ustar Description: Removes trailing newlines from standard inputs.
Author: Giorgio Maccari
Bug-Debian: http://bugs.debian.org/700088
Forwarded: https://sourceforge.net/tracker/?func=detail&aid=3603900&group_id=176110&atid=875933
--- boxshade-3.3.1.old/bx_read.c 2013-02-08 15:20:14.000000000 +0100
+++ boxshade-3.3.1.new/bx_read.c 2013-02-08 15:10:52.590377053 +0100
@@ -4,7 +4,9 @@
char *Gets(char *s, size_t length) {
fflush(stdout);
- return fgets(s,length,stdin);
+ fgets(s,length,stdin);
+ strtok(s, "\n");
+ return s;
}
/*
debian/patches/series 0000644 0000000 0000000 00000000050 12105342004 012014 0 ustar kickOutGets.patch
remove-newlines.patch
debian/source/ 0000755 0000000 0000000 00000000000 12217720236 010470 5 ustar debian/source/format 0000644 0000000 0000000 00000000014 11513776437 011712 0 ustar 3.0 (quilt)
debian/copyright 0000644 0000000 0000000 00000002340 12105333006 011111 0 ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Source: ftp://www.isrec.isb-sib.ch/pub/software/unix/boxshade/3.3.1/
Files: *
Copyright: The authors or their employers, or maybe no copyright at all
License: public-domain-claim
Boxshade is completely public-domain and may be
passed around and modified without any notice to the author.
.
the authors addresses are:
.
Kay Hofmann Michael D. Baron
Bioinformatics Group BBSRC Institute for Animal Health
ISREC Pirbright, Surrey GU24 0NF
CH-1066 Epalinges s/Lausanne U.K.
Switzerland
.
C port by
.
Hartmut Schirmer
Technische Fakultaet
Kaiserstr. 2
D-24143 Kiel
Germany
.
for any comments write an E-mail to
Kay: khofmann@isrec-sun1.unil.ch
Michael: baron@bbsrc.ac.uk (though kay wrote 99% of the program and is more
likely to be of help, especially with input and output problems)
Hartmut: hsc@techfak.uni-kiel.de (don't send Kay or Michael any questions
concerning the 'C' version of boxshade)
.
(The comments after the email addresses are form the authors themselves.)
debian/tests/ 0000755 0000000 0000000 00000000000 12217720236 010332 5 ustar debian/tests/test-with-example-data 0000755 0000000 0000000 00000000755 12105360072 014551 0 ustar #!/bin/sh -e
# Create a temporary file
TEST_OUTPUT=$(mktemp)
# Run on alignments in MSF or ALN format, and compare to reference ASCII output.
boxshade -in=/usr/share/doc/boxshade/examples/input.msf -out=$TEST_OUTPUT -def -dev=b > /dev/null
diff $TEST_OUTPUT /usr/share/doc/boxshade/examples/output.txt
boxshade -in=/usr/share/doc/boxshade/examples/input.msf -out=$TEST_OUTPUT -def -dev=b > /dev/null
diff $TEST_OUTPUT /usr/share/doc/boxshade/examples/output.txt
# Clean
rm $TEST_OUTPUT
debian/tests/control 0000644 0000000 0000000 00000000036 12105344417 011733 0 ustar Tests: test-with-example-data
debian/input.msf 0000644 0000000 0000000 00000000577 12105331363 011042 0 ustar test.msf MSF: 20 Type: N January 01, 1776 12:00 Check: 7596 ..
Name: Seq1 Len: 20 Check: 5696 Weight: 1.00
Name: Seq2 Len: 20 Check: 6211 Weight: 1.00
Name: Seq3 Len: 20 Check: 5689 Weight: 1.00
//
Seq1 GTSAGILPER THKKNMIE..
Seq2 GSS.GLLPEK THRRNMIELY
Seq3 GTTGGAAPSK THSRNMIDAI
debian/watch 0000644 0000000 0000000 00000000126 10663355636 010233 0 ustar version=3
ftp://www.isrec.isb-sib.ch/pub/software/unix/boxshade/ ([\d\.]+)\.([\d\.]+)
debian/menu 0000644 0000000 0000000 00000000202 10650302741 010045 0 ustar ?package(boxshade):\
needs="text"\
section="Applications/Science/Biology"\
title="Boxshade"\
command="/usr/bin/boxshade"
debian/changelog 0000644 0000000 0000000 00000012356 12217720161 011046 0 ustar boxshade (3.3.1-8) unstable; urgency=low
* debian/patches/remove-newlines.patch: restores interactive use.
Thanks: Giorgio Maccari. Closes: #700088.
* debian/control:
- normalised with 'cme fix dpkg-control';
- removed obsolete DM-Upload-Allowed field;
- normalised VCS URLs.
* Added example data and output, and basic regression tests.
* Machine-readable Debian copyright file.
* Use Debhelper 9, verbosely.
* Pass dpkg build flags through debian/rules.
* Removed obsolete instructions about the quilt patch system.
* Added command line parameters to manual page.
* Conforms to Policy 3.9.4.
-- Charles Plessy Mon, 23 Sep 2013 10:58:52 +0900
boxshade (3.3.1-7) unstable; urgency=low
* debian/install: Make sure boxshade executable will be installed
in the proper location
Closes: #683375 (LP: #1017188)
-- Andreas Tille Tue, 31 Jul 2012 11:17:22 +0200
boxshade (3.3.1-6) unstable; urgency=low
[ Mathieu Malaterre ]
* debian/get-orig-source: Add GZIP="--no-name" option to enable identical
tarballs
[ A. Costa ]
* Corrected spelling in debian/boxshade.1.xml. Closes: #650473.
[ Andreas Tille ]
* debian/control:
- Standards-Version: 3.9.2 (no changes needed)
- Fixed Vcs fields
* Debhelper 8 (control+compat)
* debian/bin/boxshade
- moved debian/boxshade.sh to this location to enable easier
usage of dh_install
- s#/bin/bash#/bin/sh#
* debian/install
- make use of dh_install
* debian/manpages
* debian/rules: Rewritten do use dh to profit easily from general
changes
-- Andreas Tille Sat, 07 Jan 2012 09:00:33 +0100
boxshade (3.3.1-5) unstable; urgency=low
[ David Paleino ]
* Removed myself from Uploaders
[ Andreas Tille ]
* debian/control
- Standards-Version: 3.9.1 (no changes needed)
- Debhelper 7
- Fix spelling of Debian Med in maintainer address
* debian/rules: s/dh_clean -k/dh_prep/
* debian/source/format: 3.0 (quilt)
-- Andreas Tille Fri, 14 Jan 2011 08:27:01 +0100
boxshade (3.3.1-4) unstable; urgency=low
[ Charles Plessy ]
* Updated my email address.
[ Steffen Moeller ]
* Eliminated use of gets from source
* boxshade bails out with an error if there is an error and does not
expect sudden user input ... it is scriptable now.
-- Steffen Moeller Sun, 27 Apr 2008 16:56:02 +0900
boxshade (3.3.1-3) unstable; urgency=low
[ David Paleino ]
* debian/boxshade.1 has been statically generated: this saves some
time (and space) on buildds (leaving the XML version for future
editing)
* debian/control:
- B-D updated (manpage is not generated on buildds anymore)
- added myself to Uploaders
- XS-Vcs-* moved to Vcs-* and fixed
- Homepage field now replaces the old pseudo-field in the long
description
- removed XS- from DM-Upload-Allowed
* debian/rules:
- reflecting static generation of boxshade.1 -- removing boxshade.1
target
- some general cleanup
* debian/README.Debian updated: the new debian-med.alioth.d.o website
is now mentioned.
[ Nelson A. de Oliveira ]
* Added watch file.
[ Andreas Tille ]
* Added myself to uploaders
* Added path to dh_installman
* Moved additional shellscript wrapper boxshade.sh to debian dir
* Added debian/get-orig-source script and added get-orig-source
target to debian/rules
-- Andreas Tille Tue, 26 Feb 2008 07:28:42 +0100
boxshade (3.3.1-2) unstable; urgency=low
[Charles Plessy]
* Debian Menu transition: Apps/Science becomes Applications/Science/Biology.
* makefile.unx : changes managed using the `quilt' patch system.
* makefile.unx : commenting `LDFLAGS= -s' so that stripping is handled by
dh_strip (Closes: #436605).
* debian/rules : `ifeq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS)))' test
removed because dh_strip can work without.
[Steffen Moeller]
* Updated README.Debian with reference to Debian-Med
* Updated email address to moeller@debian.org
-- Charles Plessy Thu, 9 Aug 2007 10:38:31 +0900
boxshade (3.3.1-1) unstable; urgency=low
[ Steffen Moeller ]
* Removed [biology] tag from description
[ Charles Plessy ]
* New version number, but upsteams' 3.3.1 was already packaged in Debian
under number 3.1.1 (Closes: #385255).
* Swiching to collaborative maintainance: Maintainer is a mailing-list,
Uploaders are real people.
* Tidying the package:
- Using debhelper v5 and conforming to policy 3.7.2.
- Updated manpage using the template of docbook-xsl 1.71.0.dfsg.1-1.1.
- Converted the manpage to unicode.
- Relicenced the manpage to "same licence as Boxshade itself", with the
agreement of Steffen.
- Added XS-Vcs-Svn and XS-Vcs-Browser to debian/control.
- Removed empty files debian/dirs, debian/install, debian/conffiles.
* Replaced clustalw (non-freee) by kalign (free)|clustalw in the Suggests field.
* Changed priority to optional.
-- Charles Plessy Sun, 25 Feb 2007 08:47:18 +0900
boxshade (3.1.1-1) unstable; urgency=low
* Initial Release (Closes: #234923).
-- Steffen Moeller Thu, 26 Feb 2004 13:17:22 +0100
debian/output.txt 0000644 0000000 0000000 00000000120 12105331363 011255 0 ustar Seq1 GTSAGILPERTHKKNMIE..
Seq2 -s-.-l---k--rr----LY
Seq3 --tg-aa-sk--sr---dAI
debian/input.aln 0000644 0000000 0000000 00000000300 12105331363 011007 0 ustar CLUSTAL W(1.5) multiple sequence alignment
Seq1 GTSAGILPERTHKKNMIE..
Seq2 GSS.GLLPEKTHRRNMIELY
Seq3 GTTGGAAPSKTHSRNMIDAI
*.. * * .** .***.
debian/get-orig-source 0000644 0000000 0000000 00000001027 11570214572 012130 0 ustar #!/bin/sh -e
set -e
# set -x
NAME=boxshade
VERSION=3.3.1
UTARBALL=source.tar.Z
downloadurl=ftp://www.isrec.isb-sib.ch/pub/software/unix/boxshade/3.3.1/
TMPDIR=../tarballs
mkdir -p "$TMPDIR"
cd "$TMPDIR"
if [ -e ${UTARBALL} ] ; then
echo "Using existing tarball ${UTARBALL}"
else
wget --quiet ${downloadurl}/${UTARBALL}
fi
DISTDIR=${NAME}-${VERSION}
mkdir -p ${DISTDIR}
cd ${DISTDIR}
tar -xzf ../"$UTARBALL"
cd ..
GZIP="--best --no-name" tar -czf "$NAME"_"$VERSION".orig.tar.gz "$NAME"-"$VERSION"
rm -rf "$NAME"-"$VERSION"
debian/manpages 0000644 0000000 0000000 00000000013 11702000225 010663 0 ustar debian/*.1
debian/install 0000644 0000000 0000000 00000000146 12005722576 010566 0 ustar debian/bin usr
boxshade usr/lib/boxshade
*.grp etc/boxshade
*.par etc/boxshade
*.sim etc/boxshade
debian/examples 0000644 0000000 0000000 00000000130 12105354250 010716 0 ustar debian/input.aln
debian/input.msf
debian/output.txt
debian/tests/test-with-example-data
debian/control 0000644 0000000 0000000 00000003002 12105353577 010574 0 ustar Source: boxshade
Maintainer: Debian Med Packaging Team
Uploaders: Steffen Moeller ,
Charles Plessy ,
Andreas Tille
Section: science
Priority: optional
Build-Depends: debhelper (>= 9)
Standards-Version: 3.9.4
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/boxshade/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/boxshade/trunk/
Homepage: http://www.ch.embnet.org/software/BOX_form.html
XS-Testsuite: autopkgtest
Package: boxshade
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
Suggests: seaview,
kalign | clustalw | mafft | hmmer,
xfig,
texlive-latex-extra
Description: Pretty-printing of multiple sequence alignments
Boxshade is a program for creating good looking printouts from
multiple-aligned protein or DNA sequences. The program does not perform
the alignment by itself and requires as input a file that was created
by a multiple alignment program or manually edited with respective tools.
.
Boxshade reads multiple-aligned sequences from either PILEUP-MSF,
CLUSTAL-ALN, MALIGNED-data and ESEE-save files (limited to a maximum
of 150 sequences with up to 10000 elements each). Various kinds of
shading can be applied to identical/similar residues. Output is written
to screen or to a file in the following formats: ANSI/VT100, PS/EPS,
RTF, HPGL, ReGIS, LJ250-printer, ASCII, xFIG, PICT, HTML
debian/README.Debian 0000644 0000000 0000000 00000001707 11054126367 011241 0 ustar boxshade for Debian
-------------------
This program is not perfect. If it runs smoothly, though, then it produces
nice results.
The web interface for boxshade is available for download
on ftp://www.isrec.isb-sib.ch/pub/software/unix/boxshade/www/box_www.tar.Z
It is not yet debinanised, please request this package and
explain your demand for it or use it on
http://www.ch.embnet.org/software/BOX_form.html
For LaTeX users the inspection of the TeXshade package may be of interest
which is comining in the Debian package texlive-latex-extra.
This package has its roots in the Debian-Med Custom Debian Distribution,
which features many more software packages in Bioinformatics, Medical
Informatics and e-Health:
Project page: http://www.debian.org/devel/debian-med/
Wiki page: http://wiki.debian.org/DebianMed
Live activity page: http://debian-med.alioth.debian.org/
-- Steffen Moeller , Fri, 10 Aug 2007 21:34:23 +0100
debian/boxshade.1 0000644 0000000 0000000 00000051266 12105353320 011051 0 ustar '\" t
.\" Title: BOXSHADE
.\" Author: Kay Hofmann
.\" Generator: DocBook XSL Stylesheets v1.76.1
.\" Date: February 09, 2013
.\" Manual: Boxshade Manual
.\" Source: boxshade 3.3.1
.\" Language: English
.\"
.TH "BOXSHADE" "1" "February 09, 2013" "boxshade 3.3.1" "Boxshade Manual"
.\" -----------------------------------------------------------------
.\" * 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"
boxshade \- Pretty\-printing of multiple sequence alignments
.SH "SYNOPSIS"
.HP \w'\fBboxshade\fR\ 'u
\fBboxshade\fR
.SH "DESCRIPTION"
.PP
\fBBOXSHADE\fR
is a program for pretty\-printing multiple alignment output\&. The program itself doesn\*(Aqt do any alignment, you have to use a multiple alignment program like ClustalW or Pileup and use the output of these programs as input for BOXSHADE\&.
.PP
\fB\-help\fR
.RS 4
Show the help\&.
.RE
.PP
\fB \-check \fR
.RS 4
Show the help and extend command line\&.
.RE
.PP
\fB \-def \fR
.RS 4
Use defaults, no unnecessary questions\&.
.RE
.PP
\fB \-numdef \fR
.RS 4
Use default numbering\&.
.RE
.PP
\fB \-dna \fR
.RS 4
Assume DNA sequences, use
box_dna\&.par\&.
.RE
.PP
\fB \-split \fR
.RS 4
Create separate files for multiple pages\&.
.RE
.PP
\fB \-toseq=\fR\fB\fIxxx\fR\fR\fB \fR
.RS 4
Shading according to sequence No\&.
\fIxxx\fR\&.
.RE
.PP
\fB \-in=\fR\fB\fIxxxxx\fR\fR\fB \fR
.RS 4
\fIxxxxx\fR
is input file name\&.
.RE
.PP
\fB \-out=\fR\fB\fIxxxxx\fR\fR\fB \fR
.RS 4
\fIxxxxx\fR
is output file name\&.
.RE
.PP
\fB \-par=\fR\fB\fIxxxxx\fR\fR\fB \fR
.RS 4
\fIxxxxx\fR
is parameter file name\&.
.RE
.PP
\fB \-sim=\fR\fB\fIxxxxx\fR\fR\fB \fR
.RS 4
\fIxxxxx\fR
is file name for similar residues def\&.
.RE
.PP
\fB \-grp=\fR\fB\fIxxxxx\fR\fR\fB \fR
.RS 4
\fIxxxxx\fR
is file name for grouping residues def\&.
.RE
.PP
\fB \-thr=\fR\fB\fIx\fR\fR\fB \fR
.RS 4
\fIx\fR
is the fraction of sequences that must agree for a consensus\&.
.RE
.PP
\fB \-dev=\fR\fB\fIx\fR\fR\fB \fR
.RS 4
\fIx\fR
is output device class (see below)\&.
.RE
.PP
\fB \-type=\fR\fB\fIx\fR\fR\fB \fR
.RS 4
\fIx\fR
is input file format (see below)\&.
.RE
.PP
\fB \-ruler \fR
.RS 4
Print ruler line\&.
.RE
.PP
\fB \-cons \fR
.RS 4
Create consensus line\&.
.RE
.PP
\fB \-symbcons=\fR\fB\fIxyz\fR\fR\fB \fR
.RS 4
\fIxyz\fR
are consensus symbols\&.
.RE
.PP
\fB \-symbcons="\fR\fB\fIxyz\fR\fR\fB" \fR
.RS 4
If the one above does not work, try this one\&.
.RE
.PP
\fB \-unix \fR
.RS 4
Output files lines are terminated with LF only\&.
.RE
.PP
\fB \-mac \fR
.RS 4
Output files lines are terminated with CR only\&.
.RE
.PP
\fB \-dos \fR
.RS 4
Output files lines are terminated with CRLF\&.
.RE
.PP
This manual page was written for the
Debian(TM)
distribution because the original program does not have a manual page\&. The presented information comes from the documentation of the Web Service of the 3\&.21 version that is not available as a Debian package\&.
.PP
BOXSHADE is a program for creating good looking printouts from multiple\-aligned protein or DNA sequences\&. The program does no alignment by itself, it has to take as input a file preprocessed by a multiple alignment program or a multiple file editor\&. See below for a list of supported input formats and output devices\&. In the standard BOXSHADE output, identical and similar residues in the multiple\-alignment chart are represented by different colors or shadings\&. There are some more options concerning the kind of shading to be applied, sequence numbering, consensus output and so on\&. The user interface is a bit clumsy at the moment, one has to answer a lot of questions in order to get the desired output\&. There is, however, the possibility to use default parameters from a standard parameter file or to supply the program with parameters from the command line\&. At the moment, the VMS and DOS versions of BOXSHADE have identical user interfaces\&.
.SS "Input formats"
.PP
BOXSHADE 3\&.2 knows about the following input file formats: (some of the are generally used only for MSDOS or VMS systems) + CLUSTAL and CLUSTALV, multiple alignment program, DOS/VMS/MAC default extension \&.ALN + ESEE, multiple sequence editor, DOS default extension \&.ESE + PHYLIP, phylogenetic analysis package, DOS, VMS, UNIX default extension \&.PHY + PILEUP and PRETTY of the GCG sequence analysis package VMS/UNIX default extensions \&.MSF and \&.PRE NB!! you are strongly encouraged NOT to use the PRETTY format as input, it may be incompatible with the revised version of \&.MSF input\&. We can\*(Aqt actually think why anyone would use this format now, \&.MSF files are more useful generally\&. + MALIGNED, multiple sequence editor, VMS only default extension \&.MAL BOXSHADE tries to determine the file type from the extension but will work also if different extensions are used\&.
.SS "Output devices"
.PP
POSTSCRIPT/EPS creates POSTSCRIPT(TM) files for printing on a Laserprinter or for further conversion with a POSTSCRIPT interpreter (like GHOSTSCRIPT) + HPGL for export to various graphics programs or for conversion/printing with the shareware program PRINTGL\&. Plotting BOXSHADE output on a plotter is generally not recommended + RTF for export to various word\-processing and graphics programs + CRT, uses direct screen writes to the PC\-monitor\&. Possible options depend on the graphics adapter used\&. This output device is supported only in the MSDOS version\&. + ANSI\&. On a PC, this option uses an ANSI device driver (ANSI\&.SYS) that has to be loaded in CONFIG\&.SYS previously\&. Possible character renditions are reverse, bold,underlined, blinking etc\&. On non\-DOS systems, this option behaves more or less like the VT100 output mode\&. + VT100 for display on a VT100 compatible terminal or emulator\&. + ReGISterm for display on a ReGIS compatible graphics terminal or emulator\&. + ReGISfile for later conversion by the program RETOS (copyright DEC) in order to print on DIGITALs printer series\&. + LJ250 for printing on DIGITALS LJ250 color printer\&. + ASCII output showing either the conserved residues or the varying ones (others as \*(Aq\-\*(Aq)\&. + FIG file for xfig 2\&.1\&. + PICT files for import to Mac and PC graphics progs\&. Some of the formats above offer the possibility of scaling the characters and of rotating the plot\&. Character size has to be entered in \*(Aqpoint\*(Aq units\&. Normal output orientation is in portrait mode (PS/EPS/HPGL/PICT only), to obtain output in landscape orientation, \*(Aqrotate plot = y\*(Aq has to be chosen\&. When creating multi\-page output, all pages are contained in a single output file\&. If one page per file is desired, one has to use the command line parameter /SPLIT\&. This is enforced when requesting EPSF or PICT file output, as multi\-page EPSFs are a contradiction of the purpose of an EPSF and large PICT files would probably be too big for most personal computers\&. While using the terminal as output device, the \*(AqRETURN\*(Aq key has to be pressed to obtain the next page of output\&.
.SS "Sequence numbering"
.PP
Starting with version 2\&.2 there is the possibility to add numbering to the output files\&. The numbers are printed between the sequence names and the sequence itself\&. Since most of the input\-files either use no numbering or number the first position in the alignment always with a "1" (and that does not necessarily reflect the numbers within the original sequence), the user is asked to enter the starting position for each sequence\&. The command line flag /DEFNUM suppressed that question, a starting position of 1 is assumed for all sequences\&. Boxshade starts with the value entered for the leftmost position and continues numbering every valid symbol, skipping blanks, \*(Aq\-\*(Aq,\*(Aq\&.\*(Aq and stuff like that\&.
.SS "Default parameters"
.PP
Several people using previous releases of BOXSHADE pointed me to the need of having default parameters for the various questions asked by the program\&. They argued that most sites only use one type of input files, one output device and one choice of colors for the output\&. I therefore added a management of default parameters allowing two levels of assistance to the user\&. 1) all default parameters are contained in an ASCII file that can be modified easily to accommodate the users taste\&. The format is roughly documented within the file\-header, it resembles the keyboard input one has to make if using the program interactively\&. There are two such files supplied with this release of BOXSHADE, BOX_DNA\&.PAR and BOX_PEP\&.PAR , holding some example parameters for peptide and dna\-comparisons\&. there are no big differences between these two, the major one is that when shading DNA\-comparisons one doesn\*(Aqt care of "similar" residues\&. 2) to run the program with minimal user interaction, I have added the possibility to use command line parameters\&. At the moment, you can use: /check : list all allowed command line parameters (this list) and allows parameters to be added\&. /def : program runs without questions, BOX_PEP\&.PAR is used as default /dna : makes the program use BOX_DNA\&.PAR as parameter file /pep : makes the program use BOX_PEP\&.PAR as parameter file /in=xxx : makes the program take xxx as input file /out=yyy : makes the program take yyy as output file (note1) /par=zzz : makes the program use zzz as a default parameter file /type=1 : makes the program assume an input file of type 1 (PRETTY/MSF) /dev=1 : makes the program assume and output device of type 1 (CRT) /numdef : use default numbering (all sequences starting with "1") /thr : threshold fraction of residues that must agree for a consensus /split : forces one page per file output, creates multiple output files\&. /cons : makes the program create an additional consensus line (see below) /symbcons=: influences the way the consensus line is displayed\&. (see below) /unix : writes output files in unix style (LF only) (note2) /dos : writes output files in DOS style (CR/LF) (note2) note1: on unix machines, use out=OUTPUT for terminal output on DOS machines, use out=con: on VMS machines, use out=tt: note2: if no mode is specified, the native style of the machine is used\&.
.if n \{\
.sp
.\}
.RS 4
.it 1 an-trap
.nr an-no-space-flag 1
.nr an-break-flag 1
.br
.ps +1
\fBATTENTION\fR
.ps -1
.br
.PP
on unix systems, the dash (\-) instead of the slash (/) has to be used as separation character for command line parameters\&. For example, a valid unix command line is:
\fBboxshade \-def \-numdef \-cons \-symbcons=" \&.*"\fR
.sp .5v
.RE
.SS "Shading strategies (similarity to consensus or single sequence)"
.PP
Starting with version 3, BOXSHADE has a new shading system\&. The first difference is the introduction of a threshold fraction of residues that must agree for there to be a consensus\&. Previously, the program assumed that SOME residue was always the consensus\&. If no two residues were the same, the first sequence provided the consensus residue\&. This threshold fraction can be any number between 0\&.0 and 1\&.0\&. The number of sequences that must agree for there to be a consensus is, as you might expect, this fraction times the total number of sequences in the alignment (fractions of a sequence count as one, e\&.g\&. 3\&.2 becomes 4)\&. The second difference is the idea of \*(Aqconsensus by similarity\*(Aq; this tries to take account of the situations where all the sequences may have (for example) R or K at a position, but neither in a majority\&. It would not be logical to shade one type of residue as \*(Aqidentical\*(Aq and the other as \*(Aqsimilar\*(Aq; the threshold function might also eliminate both as being in too small numbers\&. Therefore, if there is not a single residue that is conserved (greater than the threshold) at a position, the program looks for a \*(Aqgroup\*(Aq of amino acids that fulfills the requirements\&. \*(AqGroups\*(Aq are defined in the \&.grp files\&. Users can tailor these to their personal prejudices\&. Any amino acid not listed is assumed not to be in a group\&. All members of a group are considered to be mutually similar, unlike the \&.sim files, described below\&. If consensus by similarity is found, all the residues in the consensus are shaded using the \*(Aqsimilar\*(Aq shading defined by the user\&. If the user does not select \*(Aqshading by similarity\*(Aq, only identity\-type consensus is looked at\&. If an identity\-type consensus is found, and similarity shading is in operation, the program looks to see if the remaining residues are similar to the consensus residue\&. Here the box_xxx\&.sim files are used\&. The main difference between relationships in these files and those in the \&.grp files is that, e\&.g\&. in a \&.grp file the line STA means that all three a\&.a\&.s are mutually similar\&. In a \&.sim file S TA means that both T and A are considered similar to S, where there is a conserved S residue in more than threshold number of sequences\&. However, it does NOT mean that T and A are similar to each other\&. Note that cases where two residues, or groups of residues, fulfill the threshold requirements (as could happen with values of the thr\&. fraction less than or equal to 0\&.5) are treated as having no consensus\&. This describes the main shading model \*(Aqshading according to a consensus\*(Aq\&. The alternative model is called \*(Aqshading according to a master sequence\*(Aq\&. In this case the user is prompted for a sequence of the alignment and consecutively that sequence is taken to be the \*(Aqconsensus\*(Aq\&. Only those residues become shaded that are identical or similar to the chosen sequence\&. Output obtained with this option tends to be less shaded and neglects similarities between the other (non\-chosen) sequences\&. Starting in V2\&.7, this \*(Aqmaster sequence\*(Aq can be hidden\&. Thus, it only influences the shading of the other sequences without being shown itself\&.
.SS "Consensus display"
.PP
Starting with version 2\&.5, BOXSHADE offers the possibility to create an additional line holding a consensus symbol\&. This line can either be obtained by using the command line qualifier /CONS or interactively by answering the question \*(Aq create consensus? \*(Aq\&. The way this consensus line is displayed can be modified by the command line parameter SYMBCONS=xyz, by editing the respective entry in the \&.PAR file or interactively\&. Since the SYMBCONS syntax is not intuitive, here a brief description: The SYMBCONS parameter consist of exactly three symbols: + the first one stands for \*(Aqnormal\*(Aq sequence residues that are not involved in any similar/identical relationship\&. + the second symbol represents positions that are similar in all sequences of the alignment\&. See the files BOX_PEP\&.SIM and BOX_DNA\&.SIM to see what residues are considered similar\&. + the third symbol represents positions that are identical in all sequences of the alignment\&. A SYMBCONS parameter string " \&.*" (blank/point/asterisk) means: label all positions in the alignment with totally identical residues by an asterisk, all positions with all similar residues by a point and do not mark the other positions\&. The letter \*(AqB\*(Aq can be used instead of the blank, this is necessary e\&.g\&. when using the command line option /SYMBCONS=B\&.* which gives the same result as the above example\&. The option /SYMBCONS= \&.* would result in an unexpected behaviour because MSDOS squeezes blanks out of the command line\&. Besides points, asterisks and other symbols, there are two special characters when they appear in the SYMBCONS string: \*(AqL\*(Aq and \*(AqU\*(Aq\&. An \*(AqL\*(Aq means, that a lowercase representation of the most abundant residue at that position is to be used instead of a fixed consensus symbol while an \*(AqU\*(Aq means an uppercase character representation of that residue\&. A possible application would be the SYMBCONS string " LU" where similar residues are represented by lowercase characters and identical by uppercase characters\&.
.SS "Shareware/PD programs useful in conjunction with BOXSHADE"
.PP
multiple alignment files that to be used by BOXSHADE can be created, amongst others, by the following PD/freeware programs: + PHYLIP by Joe Felsenstein, available by ftp from anthro\&.utah\&.edu + ESEE by Eric Cabot, available from the same sources as BOXSHADE (see above) + CLUSTAL by Des Higgins, ditto for preview/conversion of POSTSCRIPT files, the program GHOSTSCRIPT from GNU software foundation is highly recommended\&. It is available from all major MSDOS ftp\-sites (e\&.g\&. SIMTEL or ftp\&.uni\-koeln\&.de) There is also a version tested for use with boxshade available at vax0\&.biomed\&.uni\-koeln\&.de although this might be not the most recent release\&. for Mac users, there is MacGhostscript, also available from the main archives (info\-mac, umich and their mirrors)\&. A *very* good tool for putting a preview image into an EPSF file, often a prerequisite for incorporating into a drawing package, is PS2EPS, by Peter Lerup\&. This can be found on info\-mac\&. for preview/conversion of HPGL files, the shareware program PRINTGL 1\&.18 by Cary Ravitz is highly recommended\&. It is available from many MSDOS ftp sites and from netserv@embl\-heidelberg\&.de \- output on dot printers \- Since PRINTGL offers a broad choice of printer types and is a nice program, I recommend its use for printing BOXSHADE output on non\-POSTSCRIPT printers\&. Use HPGL output with options 0F1N for normal residues 2F1N for identical residues 3F1N for similar residues 2F4N for conserved residues 8 for character size not rotated (these are the standard parameters in BOX_PEP\&.PAR) for creating a HPGL files\&. (lets call it TEST\&.PLT) Now use PRINTGL either interactively by calling PMI or use a command line like: PRINTGL /Fx/S0340/Waaac/Ptest\&.plt where test\&.plt is to be replaced by the filename to convert and the x in the expression /Fx is to be replaced by the letter of the printer you use\&. (See the PRINTGL documentation for further details)
.SH "RESTRICTIONS"
.PP
The RTF output and PHYLIP input implementations are still experimental\&. Please tell me of your experiences with the program\&. + the current DOS version supports only 13 sequences with 2000 residues each\&. This parameters can be easily changed in the source code\&. If you cannot compile the sources because you are lacking a pascal compiler, contact the author for precompiled versions
.SH "CITING BOXSHADE"
.PP
There is no publication on BOXSHADE and none is planned\&. Most people just use it for figures in publications and don\*(Aqt mention anything, this is ok for the authors of BOXSHADE\&. If you really feel like mentioning BOXSHADE, you could either acknowledge it in the figure legend or in the Mat&Meth part on sequence analysis\&.
.SH "SEE ALSO"
.PP
/etc/boxshade/*\&.par
.PP
\fBseaview\fR(1)
\fBkalign\fR(1)
.SH "AUTHORS"
.PP
\fBKay Hofmann\fR <\&kay\&.hofmann@memorec\&.com\&>
.br
ISREC, Bioinformatics Group,
CH\-1066
Epalinges s/Lausanne Switzerland
.RS 4
Wrote Boxshade\&.
.RE
.PP
\fBMichael Baron\fR <\&michael\&.baron@bbsrc\&.ac\&.uk\&>
.br
BBSRC Institute for Animal Health,
Pirbright,
Surrey
GU24 0NF
U\&.K\&.
.RS 4
Wrote Boxshade\&.
.RE
.PP
\fBHarmut Schirmer\fR <\&hsc@techfak\&.uni\-kiel\&.de\&>
.br
Technische Fakultaet,
Kaiserstr\&. 2
D\-24143
Kiel
Germany
.RS 4
C port of Boxshade\&. (don\*(Aqt send Kay or Michael any questions concerning the \*(AqC\*(Aq version of boxshade)
.RE
.PP
\fBSteffen Möller\fR <\&moeller@debian\&.org\&>
.RS 4
Wrote the manpage\&.
.RE
.PP
\fBCharles Plessy\fR <\&plessy@debian\&.org\&>
.RS 4
Updated the manpage
.RE
.SH "COPYRIGHT"
.br
Copyright \(co 1997 Kay Hofmann, Michael Baron and Harmut Schirmer
.br
Copyright \(co 2003, 2007 Steffen Moeller, Charles Plessy
.br
.PP
The above copyright notices refer to the program and its manpage respectively\&.
.PP
BOXSHADE is completely public\-domain and may be passed around and modified without any notice to the authors\&.
.PP
This manual page was written for the
Debian(TM)
system but may be used by others\&. Permission is granted to copy, distribute and/or modify this document under same terms as boxshade itself\&.
.sp
debian/compat 0000644 0000000 0000000 00000000002 12105333404 010357 0 ustar 9
debian/bin/ 0000755 0000000 0000000 00000000000 12217720236 007740 5 ustar debian/bin/boxshade 0000644 0000000 0000000 00000000104 11702000225 011436 0 ustar #!/bin/sh
export BOXDIR=/etc/boxshade
/usr/lib/boxshade/boxshade $*