MAHDS_addition

This repository contains some additional software for testing and assessing MAHDS.

Contents

(It is assumed that all paths begin with the root of the repository)

fmax

Location: fmax/.
Installation: cd fmax && make.
Input (command line parameters): path to alignment in FASTA format (required), paths to configuration files (optional). Note: by default configuration files are located in fmax/install/cfgdir.
Output (stdout): Fmax value.

artif_seq_gen

Location: testing_utils/artificial_seq_tests/artif_seq_gen.py.
Installation: not required.
Input (command line parameters): path to configuration file (optional). Note: by default configuration file is testing_utils/artificial_seq_tests/asg_config.json.
Output (files): files in FASTA format containing sequences with given parameters.

EMBL-EBI_test

Location: testing_utils/EMBL-EBI_methods/EMBL-EBI_test.py.
Installation: not required.
Input (command line parameters): path to configuration file (optional). Note: by default configuration file is testing_utils/EMBL-EBI_methods/eet_config.json.
Output (files): files in FASTA format containing multiple alignments built by services provided by EMBL-EBI.

rnd_seq_gen

Location: testing_utils/rnd_sequences/rnd_seq_gen.py.
Installation: not required.
Input (command line parameters): path to configuration file (optional). Note: by default configuration file is testing_utils/rnd_sequences/rsg_config.json.
Output (files): files in FASTA format containing sequences with given parameters.

get_di_stat

Location: testing_utils/stat_del-ins/get_di_stat.py.
Installation: not required.
Input (command line parameters): path to alignment in FASTA format (required).
Output (stdout): number of gaps and gap openings in given alignment.