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Phylogenetic visualizations

Project description

Empress is still in early development and new features to add are currently being explored. If you would like to suggest something you can email kcantrel@ucsd.edu.

# Installation Please install the following packages in order to run Empress

` conda create -n empress pip tornado source activate empress conda install -c conda-forge scikit-bio pip install git+https://github.com/biocore/empress.git `

# Run Type the following commands in the terminal for more information

` empress --help `

A bit of preprocessing occurs after empress is ran. The following message will appear in the terminal when empress is ready to be used.

` build web server server started at port 8080 `

Then enter the following in a browsers search bar to launch empress.

` http://localhost:8080/ `

# Input Formats Empress takes in as input a Newick file for the tree and a tabular mapping file for the feature metadata.

An example of a feature metadata file would look like something as follows

` ID           Genome_size     Phyla OTU_1001     100000          Proteobacteria OTU_1002     150201          Firmicutes OTU_2001     502051          Actinobacteria ` The first column of the metadata files must match the ids in the newick file. In the above example ID is what the newick file would use to name the nodes.. If a node does not have a name in the newick file, empress will assign it “yid” where id is a number corresponding to its position in the tree. Note: to make processing metadata easier, empress will remane the first column of the metadata file to Node_id. So in the above example, ID will show up as Node_id in empress.

# To run sample data set To download sample data enter the following in terminal or go into data/primates and manually download the files.

` svn export https://github.com/biocore/empress.git/trunk/data `

Both leaf_metadata.txt and internal_node_metadata.txt are space delimited. To make combining the metadata files easier, empress will rename #SequenceID will show up as Node_id in empress.

Here is an exmple of how internal_node_metadata.txt if formatted.

` Node_id Intercept_effect_size   Phyl_Group[T.Lemur]_effect_size ... y0  0.02256030930979693 -0.12709112380267737 ... y1  -0.15122058716686135    0.1629544435889327 ... . . . `

To run empress type the following command from within the directory where you downloaded the data file

` empress --tree-file tree.nwk --metadata leaf_metadata.txt --additional-metadata internal_node_metadata.txt --clade-field Node_id --main-seperator " " --additional-seperator " " ` –clade-field is what empress will use in its “clade color” feature. Node_id was choosen to better demonstrate this feature.

Note: It doesn’t matter which metadata is passed in as metadata and which one is passed in as additional-metadata

After a couple of seconds the following will display in the terminal.

` build web server server started at port 8080 `

Open up a browser and type the following into the search bar.

` http://localhost:8080/ `

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