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Chart visualization for metagenomics analysis tools AMPHORA2 and AmphoraNet. Related publication:
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AmphoraVizu, Chart visualization for metagenomics analysis tools AMPHORA2 and AmphoraNet

by Csaba Kerepesi, Balázs Szalkai, Vince Grolmusz

PIT Bioinformatics Group,

***Terms of Use:***

AmphoraVizu is free software: you can redistribute it and/or modify it under the terms of
the GNU General Public License as published by the Free Software Foundation, either
version 3 of the License, or any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details:


- User Manual for AmphoraVizu:
- For any other inquiries send an Email to Csaba Kerepesi:
- AmphoraVizu webserver:

***Quick start:***

1. Open Source AmphoraVizu is a program written in Perl programming language. Perl is downloadable from
2. Use an AMPHORA2 or AmphoraNet output file as input file (sample files are available here: ) 
3. A typical command: 
perl -input example_output.txt -min_confidence 0.1 -lowest_rank 2 -min_average 0.02 -chart_type column > out.html
4. Finally open the out.html file in a web browser. 


-input: input file (AMPHORA2 output file), default: /dev/stdin
-min_confidence: minimum confidence, default: 0.1
-lowest_rank: lowest rank (1=Superkingdom, 7=Species), default: 2
-min_average: minimum average to display, default: 0.02
-chart_title: chart title (with optional HTML tags), to override default title
-chart_type: "column": Column Chart output (default), "pie": Pie chart output with averages
-chart_width: width of chart area, all CSS values are valid (default: 100%)
-chart_height: height of chart area (default: 100%)
-chart_compact: if 1, margins are decreased as much as possible (default: 0)
-html_inline: if 1, tags like <html>, <head> and <body> are omitted (default: 0)     
-miniview: 1: miniview on, 0: miniview off (default: 0)      
-sort: "avg": sorted by averages (default), "abc" sorted by alphabet
-quantify: "prop": shows the proportions of marker genes (default), "amounts": shows the exact amounts of marker genes
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