Tutorial

# Tutorial

## I. Introduction

The following sections contain a tutorial on how calculate alignment quality scores as done in [1].

[1] Pairwise vs multiple global network alignment, Vijayan, V., Krebs, E., Meng, L., and Milenković, T., under revision.

## II. Installation

Julia 0.6 needs to be installed prior to using this software. It can be installed by navigating to the base folder of this software, starting Julia, and executing the command `julia install_pnavsmna.jl`.

## III. Calculating alignment quality scores under the PEF framework

1. Start by navigating to the `examples/` directory from the base directory of this package.

2. Create a `.csv` file similar to the `test_pef_df.csv` file in the `examples/` folder, that describes the network files, alignment file, and gene ontology ground-truth files used for calculating the alignment quality scores.

3. Run the following command, which will output the alignment quality scores to the file `test_pef_outdf.csv` as a CSV table.

    julia ../bin/pnavsmna.jl pef test_pef_df.csv test_pef_outdf.csv

## IV. Calculating alignment quality scores under the MEF framework

1. Start by navigating to the `examples/` directory from the base directory of this package.

2. Create a `.csv` file similar to the `test_mef_df.csv` file in the `examples/` folder, that describes the network files, alignment file, and gene ontology ground-truth files used for calculating the alignment quality scores.

3. Run the following command, which will output the alignment quality scores to the file `test_mef_outdf.csv` as a CSV table.

    julia ../bin/pnavsmna.jl mef test_mef_df.csv test_mef_outdf.csv