Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
valloc(3)
aligned memory allocation function
textout_right_ex(3)
Writes a right aligned string on a bitmap. Allegro game programming library
textprintf_right_ex(3)
Formatted right aligned output of a string. Allegro game programming library
vmem_malloc(3), vmem_malloc()(3), vmem_calloc()(3), vmem_realloc()(3), vmem_free()(3), vmem_aligned_alloc()(3), vmem_strdup()(3), vmem_wcsdup()(3), vmem_malloc_usable_size()(3)
memory allocation related functions
Bio::NEXUS::Tools::NexPlotter(3), nexplot.pl(3)
PostScript plot of tree + data table (from NEXUS infile) =head1 SYNOPSIS nexplot.pl [options] foo.nex [tree_name] > foo.ps =head1 OPTIONS -h Brief help message -d Full documentation -v Verbose mode -V Print version information and quit -f Specify output file (default: STDOUT) INFORMATION TO DISPLAY -b Turn on bootstrap values, if any -i Turn on internal node labeling -t Tree only (ignore any characters) -I Specify character block (by "Title") to be used in matrix (e.g. "dna", "protein", "intron") -m Matrix only (ignore any trees) -c Cladogram mode: (auto if no branch lengths present in tree) normal: all branch lengths equal accelerated: same as normal except OTUs are aligned at end -U Display taxa sets in color (-U "set1 color1 [set2 color2 ...]") Color options are red, orange, green, forest, aqua, blue, purple, pink, brown, gray, black PLOT FORMATTING -r Right-justify labels (default: left-justified) -C Columns of characters per block (default = 10) -T Specify tree width (longest branch; default: 10") -S Spacing (vertically) between OTUs (default: .25") -R Ratio of font height to Spacing (default: 0.8; rec: 0.5-1) -F Font to use for labels and titles -B Draw a box indicating postscriptes bounds of the plot area -g Include gray lines after OTU labels, even if -t (tree only) option is used PAGE SETUP -s Print on multiple pages, but shrink to page height -o Print on multiple pages at actual size -W Specify output page width (default: 8.5") -H Specify output page height (default: 11") -a Change page dimensions to fit plot =head1 DESCRIPTION B<This program> will read a NEXUS file and output a PostScript display of trees (one file for each tree in the tree block), as well as any character matrix (e.g. sequences) if present in the file. =head1 FILES =over 4 =back =head1 VERSION $Id: NexPlotter.pm,v 1.2 2008/06/16 19:53:41 astoltzfus Exp $
Bio::NEXUS::UnalignedBlock(3)
Represents an UNALIGNED block of a NEXUS file
Bio::Tools::Run::Alignment::Amap(3)
Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the Amap (2.0) program
Bio::Tools::Run::Alignment::Kalign(3)
Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the KALIGN program
Bio::Tools::Run::Alignment::MSAProbs(3)
Object for the calculation of a multiple sequence alignment (MSA) from a set of unaligned sequences using the MSAProbs program
Bio::Tools::Run::Alignment::Muscle(3)
Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the MUSCLE program
Bio::Tools::Run::Alignment::Probalign(3)
Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Probalign program
Bio::Tools::Run::Alignment::Probcons(3)
Object for the calculation of an iterative multiple sequence alignment from a set of unaligned sequences or alignments using the Probcons program
Bio::Tools::Run::Alignment::Proda(3)
Object for the calculation of sets of multiple sequence alignments from a set of unaligned sequences or alignments using the Proda program
GD::Text::Align(3)
Draw aligned strings
Graphics::Primitive::Aligned(3)
Role for components that care about alignment
LaTeXML::Core::Alignment(3), "LaTeXML::Core::Alignment"(3)
representation of aligned structures
Template::Plugin::GD::Text::Align(3)
Draw aligned strings in GD images
bp_search2alnblocks(1)
Turn SearchIO parseable reports(s) into a set of aligned blocks
home | help