If you mean "I know the topology and perhaps also branch lengths of a particular tree I'm interested in, and want to turn that into an (e.g. NEWICK format) tree file, whose representation I want to then manipulate in a tree viewer such as Dendroscope or FigTree"

then you could try using Mesquite http://mesquiteproject.org/mesquite/mesquite.html .

It takes some practice to get used to it, but maybe you'll find these notes I've put together on it useful http://www.embl.de/~seqanal/courses/commonCourseContent/usingMesquite.html

use Bio::TreeIO to read the tree, save it to SVG , edit it with inkscape

... or ITOL if you want a web-app and don't like to script, then save to SVG

You can use MATLAB: http://www.mathworks.com/help/bioinfo/ref/phytreeread.html http://www.mathworks.com/help/bioinfo/ref/phytree.html

Maybe SplitsTree can do what you want... There you can conveniently rotate and move clades/nodes while preserving branch lengths....and more.. It can start with all sorts of formats from distance matrices to PHILIP, nexus asf...

I recommend Bosque. You can view adn edit newick trees very easy.

http://inf.imo-chile.cl/software/bosque.html

ggtree

https://guangchuangyu.github.io/ggtree/documentation/

I would recommend PhyML for tree generation, figtree for edition and visualization and inkscape for final ajustments