Very basic phylogeny editor


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You can also use your local clone with git send-email.

#phyedit: tools for editing phylogenies

phyedit is a simple CLI phylogeny editor and do is a web app for browser-based use of phyedit


  • Gawk
  • Graphviz and GD, for creating images of the phylogeny
  • Apache web server, for web app

#Phylogeny file format

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> ]] 
    <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