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"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
author padge
date Fri, 25 Mar 2022 13:04:31 +0000
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1 .. image:: _static/img/ClipKIT_logo_top_only_v1.jpg
2 :width: 55%
3 :align: center
4 :target: https://jlsteenwyk.com/ClipKIT
5
6 ^^^^^
7
8
9 ClipKIT is a fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes those that display characteristics poor phylogenetic signal.
10
11
12 If you found clipkit useful, please cite *ClipKIT: a multiple sequence alignment trimming software for accurate phylogenomic inference*. Steenwyk et al. 2020, PLoS Biology. doi: |doiLink|_.
13
14 .. _doiLink: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001007
15 .. |doiLink| replace:: 10.1371/journal.pbio.3001007
16
17
18 Quick Start
19 -----------
20 **1) Installation**
21
22 To help ensure ClipKIT can be installed using your favorite workflow, we have made ClipKIT available from pip, source, and the anaconda cloud.
23
24 **Install from pip**
25
26 To install from pip, use the following commands:
27
28 .. code-block:: shell
29
30 # create virtual environment
31 python -m venv .venv
32 # activate virtual environment
33 source .venv/bin/activate
34 # install clipkit
35 pip install clipkit
36
37 **Note, the virtual environment must be activated to use clipkit.**
38
39 |
40
41 **Install from source**
42
43 Similarly, to install from source, we strongly recommend using a virtual environment. To do so, use the following commands:
44
45 .. code-block:: shell
46
47 # download
48 git clone https://github.com/JLSteenwyk/ClipKIT.git
49 cd PhyKIT/
50 # create virtual environment
51 python -m venv .venv
52 # activate virtual environment
53 source .venv/bin/activate
54 # install
55 make install
56
57 To deactivate your virtual environment, use the following command:
58
59 .. code-block:: shell
60
61 # deactivate virtual environment
62 deactivate
63
64 **Note, the virtual environment must be activated to use clipkit.**
65
66 .. code-block:: shell
67
68 git clone https://github.com/JLSteenwyk/ClipKIT.git
69 cd ClipKIT/
70 make install
71
72 If you run into permission errors when executing *make install*, create a
73 virtual environemnt for your installation:
74
75 .. code-block:: shell
76
77 git clone https://github.com/JLSteenwyk/ClipKIT.git
78 cd ClipKIT/
79 python -m venv .venv
80 source .venv/bin/activate
81 make install
82
83 Note, the virtual environment must be activated to use clipkit.
84
85 |
86
87 **Install from anaconda**
88
89 To install via anaconda, execute the following command:
90
91 .. code-block:: shell
92
93 conda install -c jlsteenwyk clipkit
94
95 Visit here for more information: https://anaconda.org/jlsteenwyk/clipkit
96
97 |
98
99 **2) Usage**
100
101 To use ClipKIT in its simpliest form, execute the following command:
102
103 .. code-block:: shell
104
105 clipkit <input>
106
107 Output file with the suffix ".clipkit"
108
109 |
110
111 ^^^^
112
113 .. toctree::
114 :maxdepth: 4
115
116 about/index
117 advanced/index
118 performance_assessment/index
119 change_log/index
120 other_software/index
121 frequently_asked_questions/index
122
123 ^^^^
124