tree-puzzle(1) [debian man page]
TREE-PUZZLE(1) General Commands Manual TREE-PUZZLE(1) NAME
tree-puzzle - Reconstruction of phylogenetic trees by maximum likelihood SYNOPSIS
tree-puzzle DESCRIPTION
This manual page documents briefly the tree-puzzle command. This manual page was written for the Debian GNU/Linux distribution because the original program does not have a manual page. TREE-PUZZLE is the new name for the program previously known as PUZZLE! tree-puzzle is an interactive console program that implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. TREE-PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can also be calculated under the clock-assumption. In addi- tion, TREE-PUZZLE offers a novel method, likelihood mapping, to investigate the support of a hypothesized internal branch without computing an overall tree and to visualize the phylogenetic content of a sequence alignment. There is also a paralellized version tree-ppuzzle available. OPTIONS
There are no options. For usage please look at /usr/share/doc/tree-puzzle/tree-puzzle.pdf. SEE ALSO
phylip(1), treetool(1). tree-ppuzzle(1). This manual page was written by Dr. Guenter Bechly <gbechly@debian.org>, for the Debian GNU/Linux system (but may be used by others). April 20, 2001 TREE-PUZZLE(1)
Check Out this Related Man Page
NJPLOT(1) General Commands Manual NJPLOT(1) NAME
njplot - A phylogenetic tree drawing program for biologists newicktops - draw phylogenetic trees into PostScript file SYNOPSIS
njplot [options] tree_file newicktops [options] tree_file newicktotxt [options] tree_file DESCRIPTION
This manual page documents briefly the njplot command. The newicktops command does exactly the same but needs no X11 display. The output is rendered into a PostScript file. The newicktotxt command does exactly the same as newicktops but the output is rendered into a text file. This manual page was rewritten for the Debian GNU/Linux distribution because the original program does not have a manual page. njplot is a tree drawing program able to draw any binary or multi-branched tree expressed in the standard phylogenetic tree format (e.g., the format used by the PHYLIP package). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods. Any rooting of the unrooted tree can be interactively specified using the mouse. NJplot also allows zooming, branch swapping, display of bootstrap scores and saving in the PostScript format. NJplot can therefore be used as a graphical extension of any package of phylogenetic program which employs the standard tree format for storing trees (i.e., with most such packages). OPTIONS
There are only the following options which only work in an x-terminal-emulator, but not in console mode: -h Prints out brief help. -us Postscript tree file prepared for US Letter paper size. -psonly No window interface, just write the PostScript tree file. -size n Font size n used for taxon names. -pc n number of pages for PostScript output. -psize widthxheight size of PostScript page expressed as WIDTHxHEIGHT. -lengths Show branch lengths if they appear in tree file. -boot Show bootstrap values if they appear in tree file. -notitle Don't include title in PostScript output. SEE ALSO
unrooted(1). Word-Wide-Web: http://pbil.univ-lyon1.fr/software/njplot.html AUTHOR
: Manolo Gouy e-mail: mgouy@biomserv.univ-lyon1.fr This manual page was written by Dr. Guenter Bechly <gbechly@debian.org>, for the Debian GNU/Linux system (but may be used by others). April 10, 2001 NJPLOT(1)