1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
|
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
.TH GRAPHLAN "1" "June 2016" "graphlan 1.1" "User Commands"
.SH NAME
graphlan \- circular representations of taxonomic and phylogenetic trees
.SH SYNOPSIS
.B graphlan
[\-h] [\-\-format ['output_image_format']] [\-\-warnings WARNINGS]
[\-\-positions POSITIONS] [\-\-dpi image_dpi] [\-\-size image_size]
[\-\-pad pad_in] [\-\-external_legends] [\-v]
input_tree output_image
.SH DESCRIPTION
GraPhlAn is a software tool for producing high-quality circular
representations of taxonomic and phylogenetic trees. It focuses on
concise, integrative, informative, and publication-ready representations
of phylogenetically- and taxonomically-driven investigation.
.SH OPTIONS
.SS "positional arguments:"
.TP
input_tree
the input tree in PhyloXML format
.TP
output_image
the output image, the format is guessed from the
extension unless \fB\-\-format\fR is given. Available file
formats are: png, pdf, ps, eps, svg
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-format\fR ['output_image_format']
set the format of the output image (default none
meaning that the format is guessed from the output
file extension)
.TP
\fB\-\-warnings\fR WARNINGS
set whether warning messages should be reported or not
(default 1)
.TP
\fB\-\-positions\fR POSITIONS
set whether the absolute position of the points should
be reported on the standard output. The two
cohordinates are r and theta
.TP
\fB\-\-dpi\fR image_dpi
the dpi of the output image for non vectorial formats
.TP
\fB\-\-size\fR image_size
the size of the output image (in inches, default 7.0)
.TP
\fB\-\-pad\fR pad_in
the distance between the most external graphical
element and the border of the image
.TP
\fB\-\-external_legends\fR
specify whether the two external legends should be put
in separate file or keep them along with the image
(default behavior)
.TP
\fB\-v\fR, \fB\-\-version\fR
Prints the current GraPhlAn version and exit
.SH AUTHOR
The software was written by Nicola Segata <nsegata@hsph.harvard.edu>
.P
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
|
