'\" t .\" Title: PRETTYPLOT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PRETTYPLOT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * 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" prettyplot \- Draw a sequence alignment with pretty formatting .SH "SYNOPSIS" .HP \w'\fBprettyplot\fR\ 'u \fBprettyplot\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR [\fB\-matrixfile\ \fR\fB\fImatrix\fR\fR] [\fB\-residuesperline\ \fR\fB\fIinteger\fR\fR] [\fB\-resbreak\ \fR\fB\fIinteger\fR\fR] [\fB\-ccolours\ \fR\fB\fIboolean\fR\fR] [\fB\-cidentity\ \fR\fB\fIstring\fR\fR] [\fB\-csimilarity\ \fR\fB\fIstring\fR\fR] [\fB\-cother\ \fR\fB\fIstring\fR\fR] [\fB\-docolour\ \fR\fB\fIboolean\fR\fR] [\fB\-shade\ \fR\fB\fIstring\fR\fR] [\fB\-pair\ \fR\fB\fIarray\fR\fR] [\fB\-identity\ \fR\fB\fIinteger\fR\fR] [\fB\-box\ \fR\fB\fIboolean\fR\fR] [\fB\-boxcol\ \fR\fB\fIboolean\fR\fR] [\fB\-boxuse\ \fR\fB\fIstring\fR\fR] [\fB\-name\ \fR\fB\fIboolean\fR\fR] [\fB\-maxnamelen\ \fR\fB\fIinteger\fR\fR] [\fB\-number\ \fR\fB\fIboolean\fR\fR] [\fB\-listoptions\ \fR\fB\fIboolean\fR\fR] [\fB\-plurality\ \fR\fB\fIfloat\fR\fR] [\fB\-consensus\ \fR\fB\fIboolean\fR\fR] [\fB\-collision\ \fR\fB\fIboolean\fR\fR] [\fB\-alternative\ \fR\fB\fIlist\fR\fR] [\fB\-showscore\ \fR\fB\fIinteger\fR\fR] [\fB\-portrait\ \fR\fB\fIboolean\fR\fR] \fB\-graph\ \fR\fB\fIgraph\fR\fR .HP \w'\fBprettyplot\fR\ 'u \fBprettyplot\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBprettyplot\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Multiple,Display" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequences\fR \fIseqset\fR .RS 4 .RE .PP \fB\-matrixfile\fR \fImatrix\fR .RS 4 This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&. .RE .SS "Additional section" .PP \fB\-residuesperline\fR \fIinteger\fR .RS 4 The number of residues to be displayed on each line Default value: 50 .RE .PP \fB\-resbreak\fR \fIinteger\fR .RS 4 Default value: $(residuesperline) .RE .PP \fB\-ccolours\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-cidentity\fR \fIstring\fR .RS 4 Default value: RED .RE .PP \fB\-csimilarity\fR \fIstring\fR .RS 4 Default value: GREEN .RE .PP \fB\-cother\fR \fIstring\fR .RS 4 Default value: BLACK .RE .PP \fB\-docolour\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-shade\fR \fIstring\fR .RS 4 Set to BPLW for normal shading (black, pale, light, white) so for pair = 1\&.5,1\&.0,0\&.5 and shade = BPLW Residues score Colour 1\&.5 or over\&.\&.\&. BLACK (B) 1\&.0 to 1\&.5 \&.\&.\&. BROWN (P) 0\&.5 to 1\&.0 \&.\&.\&. WHEAT (L) under 0\&.5 \&.\&.\&.\&. WHITE (W) The only four letters allowed are BPLW, in any order\&. .RE .PP \fB\-pair\fR \fIarray\fR .RS 4 Default value: 1\&.5,1\&.0,0\&.5 .RE .PP \fB\-identity\fR \fIinteger\fR .RS 4 .RE .PP \fB\-box\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-boxcol\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-boxuse\fR \fIstring\fR .RS 4 Default value: GREY .RE .PP \fB\-name\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-maxnamelen\fR \fIinteger\fR .RS 4 Default value: 10 .RE .PP \fB\-number\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-listoptions\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-plurality\fR \fIfloat\fR .RS 4 Default value: @( $(sequences\&.totweight) / 2) .RE .SS "Consensus section" .PP \fB\-consensus\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-collision\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-alternative\fR \fIlist\fR .RS 4 Values are 0:Normal collision check\&. (default) 1:Compares identical scores with the max score found\&. So if any other residue matches the identical score then a collision has occurred\&. 2:If another residue has a greater than or equal to matching score and these do not match then a collision has occurred\&. 3:Checks all those not in the current consensus\&.If any of these give a top score for matching or identical scores then a collision has occured\&. .RE .PP \fB\-showscore\fR \fIinteger\fR .RS 4 Default value: \-1 .RE .PP \fB\-portrait\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Output section" .PP \fB\-graph\fR \fIgraph\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP prettyplot is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp