Yes, graphviz can do this.
Layout a directed graph
Let's say you have the following graph in tree.gv
:
digraph g{
a[label="I"];
b[label="am"];
c[label="a"];
d[label="tree"];
e[label="with"];
f[label="7"];
g[label="nodes"];
a -> b -> c;
b -> d -> e;
d -> f;
d -> g;
}
dot
can lay out this graph: dot tree.gv
which results in
digraph g {
node [label="\N"];
graph [bb="0,0,208,252"];
a [label=I, pos="63,234", width="0.75", height="0.5"];
b [label=am, pos="63,162", width="0.75", height="0.5"];
c [label=a, pos="27,90", width="0.75", height="0.5"];
d [label=tree, pos="99,90", width="0.75", height="0.5"];
e [label=with, pos="27,18", width="0.75", height="0.5"];
f [label=7, pos="99,18", width="0.75", height="0.5"];
g [label=nodes, pos="176,18", width="0.89579", height="0.5"];
a -> b [pos="e,63,180.1 63,215.7 63,207.98 63,198.71 63,190.11"];
b -> c [pos="e,35.304,107.15 54.65,144.76 50.288,136.28 44.853,125.71 39.959,116.2"];
b -> d [pos="e,90.696,107.15 71.35,144.76 75.712,136.28 81.147,125.71 86.041,116.2"];
d -> e [pos="e,41.796,33.385 84.43,74.834 74.25,64.938 60.476,51.546 48.969,40.359"];
d -> f [pos="e,99,36.104 99,71.697 99,63.983 99,54.712 99,46.112"];
d -> g [pos="e,159.91,33.626 114.58,74.834 125.4,65.003 140,51.723 152.26,40.582"];
}
All the coordinates can be found in the output. If you need even more details on how to draw the graph, you may try using the xdot
format: dot -Txdot tree.gv
digraph g {
node [label="\N"];
graph [bb="0,0,208,252",
_draw_="c 9 -#ffffffff C 9 -#ffffffff P 4 0 -1 0 252 209 252 209 -1 ",
xdotversion="1.2"];
a [label=I, pos="63,234", width="0.75", height="0.5", _draw_="c 9 -#000000ff e 63 234 27 18 ", _ldraw_="F 14.000000 11 -Times-Roman c 9 -#000000ff T 63 228 0 5 1 -I "];
b [label=am, pos="63,162", width="0.75", height="0.5", _draw_="c 9 -#000000ff e 63 162 27 18 ", _ldraw_="F 14.000000 11 -Times-Roman c 9 -#000000ff T 63 156 0 17 2 -am "];
c [label=a, pos="27,90", width="0.75", height="0.5", _draw_="c 9 -#000000ff e 27 90 27 18 ", _ldraw_="F 14.000000 11 -Times-Roman c 9 -#000000ff T 27 84 0 7 1 -a "];
d [label=tree, pos="99,90", width="0.75", height="0.5", _draw_="c 9 -#000000ff e 99 90 27 18 ", _ldraw_="F 14.000000 11 -Times-Roman c 9 -#000000ff T 99 84 0 21 4 -tree "];
e [label=with, pos="27,18", width="0.75", height="0.5", _draw_="c 9 -#000000ff e 27 18 27 18 ", _ldraw_="F 14.000000 11 -Times-Roman c 9 -#000000ff T 27 12 0 24 4 -with "];
f [label=7, pos="99,18", width="0.75", height="0.5", _draw_="c 9 -#000000ff e 99 18 27 18 ", _ldraw_="F 14.000000 11 -Times-Roman c 9 -#000000ff T 99 12 0 7 1 -7 "];
g [label=nodes, pos="176,18", width="0.89579", height="0.5", _draw_="c 9 -#000000ff e 176 18 32 18 ", _ldraw_="F 14.000000 11 -Times-Roman c 9 -#000000ff T 176 12 0 34 5 -nodes "];
a -> b [pos="e,63,180.1 63,215.7 63,207.98 63,198.71 63,190.11", _draw_="c 9 -#000000ff B 4 63 216 63 208 63 199 63 190 ", _hdraw_="S 5 -solid c 9 -#000000ff C 9 -#000000ff P 3 67 190 63 180 60 190 "];
b -> c [pos="e,35.304,107.15 54.65,144.76 50.288,136.28 44.853,125.71 39.959,116.2", _draw_="c 9 -#000000ff B 4 55 145 50 136 45 126 40 116 ", _hdraw_="S 5 -solid c 9 -#000000ff C 9 -#000000ff P 3 43 114 35 107 37 118 "];
b -> d [pos="e,90.696,107.15 71.35,144.76 75.712,136.28 81.147,125.71 86.041,116.2", _draw_="c 9 -#000000ff B 4 71 145 76 136 81 126 86 116 ", _hdraw_="S 5 -solid c 9 -#000000ff C 9 -#000000ff P 3 89 118 91 107 83 114 "];
d -> e [pos="e,41.796,33.385 84.43,74.834 74.25,64.938 60.476,51.546 48.969,40.359", _draw_="c 9 -#000000ff B 4 84 75 74 65 60 52 49 40 ", _hdraw_="S 5 -solid c 9 -#000000ff C 9 -#000000ff P 3 51 38 42 33 47 43 "];
d -> f [pos="e,99,36.104 99,71.697 99,63.983 99,54.712 99,46.112", _draw_="c 9 -#000000ff B 4 99 72 99 64 99 55 99 46 ", _hdraw_="S 5 -solid c 9 -#000000ff C 9 -#000000ff P 3 103 46 99 36 96 46 "];
d -> g [pos="e,159.91,33.626 114.58,74.834 125.4,65.003 140,51.723 152.26,40.582", _draw_="c 9 -#000000ff B 4 115 75 125 65 140 52 152 41 ", _hdraw_="S 5 -solid c 9 -#000000ff C 9 -#000000ff P 3 155 43 160 34 150 38 "];
}
Detailed information about this format can be found on the graphviz web site.
Layout only edges / recompute edges
You may use one of the above outputs, modify positions of any nodes, and use it as input for the following command:
neato -n tree.modified.gv
This will recompute only the edges (more information on neato dot and neato options can be found on their manual pages).
Below you can see an example of an unmodified and a modified layout - I changed positions for the b and g nodes.
Automatic layout:

Modified layout:
