05 Structure of PhylUp

The PhylUp workflow consists of several classes and associated packages, that are all called by the main class PhylUp. First, all settings are being set by calling the Config package. If needed databases are not present, they will be downloaded via the db_updater. In the beginning, the InputCleaner class cleans the input. All functions related to BLAST are found in blast.py, all taxonomic conversions are being done by the ncbiTAXONparser package. Newly found sequences are being filtered by the different classes of the Sequence Filter. Finally, the AlnUpdater and TreeUpdater classes are being called.

The Concat package can be used after extending the single-locus alignments to get a concatenated dataset. Before the program can run, its dependent software tools, RAxML-NG, blast+ PaPaRa, EPA-NG, ModelTest-NG, and the blast database need to be installed. PhylUp itself depends on various python packages (Biopython, dendropy, pandas, etc.). Detailed instructions on how to install all the dependencies can be found on 01 Install PhylUp