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README.md

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Folder contents

This folder contains benchmark_result.zip and some shell scripts *.sh.

Before test

Before testing the program, please download and extract files from bench.tar.gz.

wget http://www.drive5.com/bench/bench.tar.gz
tar xvf bench.tar.gz
mv bench1.0 dataset # The shell script use dataset folder for further test

Configuring the test program

See here for configuring WMSA.

(Optional) For testing MAFFT, we recommended use conda configuration. The command of configuration like this:

conda create -n mafft
conda activate mafft
conda install mafft
mafft --help

Configuring the shell scripts

If the wmsa and MAFFT program is configured by conda, the scripts can be directly used for testing the results. Otherwise, change line 6 ( program_name ) in order to specify the location of the program.

Run shell scripts

bash *.sh dataset_name

For exapmle, running wmsa on dataset bali2dna in threshold 0.8 by typing:

bash run.wmsa.0.8.sh bali2dna

The result file is located in dataset/bali2dna/wmsa.0.8.txt .

Results

The file benchmark_result.zip contains folders, each folder contains five test results: MAFFT-FFT-NS-1 (mafft.fftns1.txt), MAFFT-FFT-NS-2 (mafft.fftns2.txt), WMSA-0.8 (wmsa.0.8.txt), WMSA-0.9 (wmsa.0.9.txt) and WMSA-0.95 (wmsa-0.95.txt) .