added license
multiphy
pretty tree
phyedit
is a simple CLI phylogeny editor and do
is a web app for
browser-based use of phyedit
Dependencies:
A pipe-delimited list of child-parent pairs. Order of the parents is uninformative, but order of children sharing a parent is preserved. All node names must be unique. No branch lengths or other node-related information. E.g.,
a|root a y
c|root / /
b|root is root --c
y|c \ \
x|c b x
$ phyedit help
Usage: phyedit [ <action> | help ] [ <node1> [ <node2> ]]
Actions
<none> : just create image
add : add terminal <node2> to <node1>
insert : add <node2> in parent edge of <node1>
rm : delete <node1> if terminal or single-daughter-node
spin : rearrange order of daughters for bifurcating <node1>
edit : change node label for <node1>
(all the above also output updated image of phylo)
newick : output Newick for input fy-format
Input file
default = phy.fy ; other files can be supplied via environment
variables PHYEDIT_DIR and PHYEDIT_FILEBASE (omit suffix .fy)
Note: If dot
(Graphviz) is not in $PATH
, create a symlink called
dot
in the same directory as phyedit
and edit the code, replacing
calls to dot
with ./dot
.
Installation as web app: within a path viewable via apache:
git clone https://github.com/camwebb/phyedit.git
cd phyedit
cp htaccess_template .htaccess
# uncomment .htaccess authentication lines, create password file with htpasswd
mkdir tmp
# if http cgi owner is not same as filesytem owner:
# chmod a+w tmp