tongjial/treekit

A toolkit for the tree manipulation

TreeKit

A toolkit for the mass trees manipulation

Dependency

• python3
• DendroPy

Installation

You can use treekit.py as a stand-alone program or clone it if you have git installed on your system

git clone https://github.com/tongjial/treekit.git

Current implementation

usage: treekit <command> [<args>] or treekit <command> -h

The options of commands are:
    summary     view trees summary
    taxa        view taxa summary
    remove      remove specific taxa/tips from trees
    keep        pick-up the trees with specific taxa
    mrca        check the monophyly or extract the clade based on given taxa/group
    extract     generate subtrees only consist of the given taxa
    prune       prune trees with specific branchlength
    root        root/reroot/unroot trees
    draw        display trees as textplot
    compare     compare trees between two different sources
Use treekit <command> -h for help with arguments of the command of interest

treekit's Issues

erro

(treekit) sxq020@masterv2:~/MJP/softward/treekit$ python treekit.py compare
Traceback (most recent call last):
File "/media/ym/desk16/sxq020/MJP/softward/treekit/treekit.py", line 810, in
main()
File "/media/ym/desk16/sxq020/MJP/softward/treekit/treekit.py", line 785, in main
kwargs = configs()
^^^^^^^^^
File "/media/ym/desk16/sxq020/MJP/softward/treekit/treekit.py", line 804, in configs
config_dict = config.get_args_dict()
^^^^^^^^^^^^^^^^^^^^^^
File "/media/ym/desk16/sxq020/MJP/softward/treekit/treekit.py", line 195, in get_args_dict
arguments = getattr(self, self.args.command)().dict
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'dict'. Did you mean: 'dir'?