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README.md

Bacterial rosegarden

Authors: Damir Melnikov, Tanya Bibikova

Bacterial rosegarden is a tool for metagenomic phylogeny visualization. The tool was implemented mostly in JavaScript using d3.js library. The tool was used in Russian Metagenomic project.

Project description

There are two branches: hyphen (default) and circles with slightly different visual layout.

In Bacterial rosegarden three types of data are used: distance matrices, bacterial phylogeny metainformation and sample metainformation.

Distance matrix is a matrix of all pairwise sample-to-sample distances.

Example:

| sample_name_1 | sample_name_2 | sample_name_3 --- | --- | --- | --- sample_name_1 | 0.0 | 0.01 | 0.02 sample_name_2 | 0.01 | 0.0 | 0.015 sample_name_3 | 0.02 | 0.015 | 0.0

Bacterial phylogeny metainformation example:

phylum class order family genus org
Verrucomicrobia Verrucomicrobiae Verrucomicrobiales Verrucomicrobiaceae Akkermansia Akkermansia_muciniphila_ATCC_BAA_835"
Bacteroidetes Bacteroidia Bacteroidales Rikenellaceae Alistipes Alistipes_indistinctus_YIT_12060
Bacteroidetes Bacteroidia Bacteroidales Rikenellaceae Alistipes Alistipes_onderdonkii_DSM_19147
Firmicutes Clostridia Clostridiales Clostridiaceae Coprococcus Clostridium_sp_L2_50

Sample metainformation can contain any information but fields sample_name, country,country_full_name and subj_id are required. subj_id is a patient identidification number. This number can be the same for different samples in case time-series data.

Sample metainformation example:

sample_name country country_full_name region subj_id
sample_1 RUS Russia Moscow 1
sample_2 RUS Russia Moscow 1
sample_3 RUS Russia Saint-Petersburg 2
sample_4 USA USA New-York 3

License

Copyright (c) 2014, Damir Melnikov, Tanya Bibikova

Permission to use, copy, modify, and/or distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies.

THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.