README.md

Distinguishing Felsenstein zone from Farris zone

Prerequisites

For all scripts Python 3.6.6 was used. The python packages used can be installed via

pip install (--user) -r packages_required.txt

if python3 and pip are already installed.

To pull the raw data from this repository, please make sure that you have Git Large File Storage installed.

Network for simulated alignments using Jukes-Cantor model

The results presented in the manuscript stem from the network F-zoneNN_2 saved in the models folder. This model can be retrained by first preprocessing the training data via

./preprocess_zone_train_data.sh

in the folder data/preprocessing and then training the network using config_F-zoneNN.yaml in the config folder

python3 mlp.py config/config_F-zoneNN.yaml

If an already trained network should be tested, first the test data has to be preprocessed by

./preprocess_zone_test_data.sh

in the folder data/preprocessing.

Testing of the network can be done by executing:

python3 test_zone.py [-h]

Network for Strepsiptera data

The results presented in the manuscript stem from the network StrepsipteraNN_3 saved in the models folder. The preprocessing for the training data

./preprocess_strepsiptera_train_data.sh

and for the test data

./preprocess_strepsiptera_test_data.sh

can both be started in the folder data/preprocessing. The same holds for the extraction of the frequencies from the Strepsiptera quartets

./preprocess_strepsiptera_real_quartets.sh

as well as for the extraction of the frequencies from the differently ordered Strepsiptera quartets

./preprocess_strepsiptera_real_quartets_permuted.sh

The network can then be trained via

python3 mlp.py config/config_StrepsipteraNN.yaml

To extract for which strepsiptera quartets the network infers a Farris-type or Felsenstein-type tree excecute

python3 test_strepsiptera_quartets.py [-h]

The output lists the number of permutations of a quartet for which the network infers a Farris-type or Felsenstein-type tree. Testing of the network on simulated data can be done by executing:

python3 test_simulated_strepsiptera_alignments.py [-h]