7 Modules

Here we provide introduction to each module along with example commands.

Please ensure that you are running the correct Python environment and execute these commands within the local project directory of iPhylo CLI.

If you choose to run them from other directories, we recommend specifying the script’s location using an absolute path.

7.1 Phylotree

The phylo tree module offers the same functionality as the iPhylo Tree online web application, but run locally.

Run the following command to see a description of the module and help about the parameters.

python iphylo.py phylotree -h

Use the following commands to start your try:

python iphylo.py phylotree -i "Homo sapiens,Mus musculus,Gallus gallus,Drosophila melanogaster,Escherichia coli"
                                
python iphylo.py phylotree -i 9606,10090,9031,7227,562 

7.2 Chemtree

This module is used to generate a taxonomic tree of chemicals, run the following command for help

python iphylo.py chemtree -h 

Use the following commands to start your try:

python iphylo.py chemtree -f 'example/inchikeys.txt' -fn 'chem\_01'

7.3 Chem Online

The exclusive online chemical module enables chemical information retrieval from ClassyFire API, including the chemicals processed with corresponding taxonomy data stored in ClassyFire’s database. Over 70 million chemicals can be queried through this online module, which is continually growing. This feature significantly augments the capabilities of chemical taxonomy analysis.

Run the following command for help:

python iphylo.py chemonline -h 

Use the following commands to have some try:

python iphylo.py chemonline -f 'example/inchikeys\_for\_online.txt' -fn 'chem\_02'

7.4 CSV2Tree

You can use this module to build a tree for any data with a hierarchy.

Use the following command for more help information:

python iphylo.py csv2tree --help

The data should be presented in a csv table, with each row representing a categorized piece of information and each column representing a categorization level.

Here is an example of statistical analysis methods:

Input table

Statistical Analysis	Hypothesis Tests	Parametric Tests	One Sample	t test
Statistical Analysis	Hypothesis Tests	Parametric Tests	One Sample	z test
Statistical Analysis	Hypothesis Tests	Parametric Tests	Two Samples	Independent Samples	Two-group t test
Statistical Analysis	Hypothesis Tests	Parametric Tests	Two Samples	Independent Samples	z test
Statistical Analysis	Hypothesis Tests	Nonparametric Tests	One Samples	Kolmogorov-Smirnov
Statistical Analysis	Hypothesis Tests	Nonparametric Tests	One Samples	Binomial
Statistical Analysis	Hypothesis Tests	Nonparametric Tests	Two Samples	Paired Samples	Wilcoxon
Statistical Analysis	Hypothesis Tests	Nonparametric Tests	Two Samples	Paired Samples	Chi-square

Output tree in Newick format

((((((Chi-square,Wilcoxon)Paired_Samples)Two_Samples,(Binomial,Kolmogorov-Smirnov)One_Samples)Nonparametric_Tests,(((z_test,Two-group_t_test)Independent_Samples)Two_Samples,(z_test,t_test)One_Sample)Parametric_Tests)Hypothesis_Tests)Statistical_Analysis);

Plot by iPhylo Visual