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QuartetScores

Code for computing various support scores for internodes.

See http://www.biorxiv.org/content/early/2017/07/27/168526 for the preprint.

EDIT: The paper has now been published in Systematic Biology: https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syz058/5556115

If you cannot find our supplementary text, please download it from here: #4

Download

We currently provide binaries for Linux and Mac systems, which are available at the Releases Page.

Please try those first. If they do not work, you find detailed build instructions in the BUILD.md document.

Command Line Options

The command line options of the program are:

./QuartetScores  [-s] [-v] [-t <number>] -r <file_path> -e <file_path> -o <file_path> [-q <file_path>] [--version] [-h]

Where:

-r <file_path>, --ref <file_path>: (required) Path to the reference tree

-e <file_path>, --eval <file_path>: (required) Path to the evaluation trees

-o <file_path>, --output <file_path>: (required) Path to the annotated newick output file (for LQIC/QPIC/EQPIC scores)

-q <file_path>, --qic <file_path>: (optional) Path to the file where to write the raw QIC scores for each quartet

-s, --savemem: Consume less memory, but with the cost of increased runtime (~50% more)

-v, --verbose: Verbose mode

-t <number>, --threads <number>: Maximum number of threads to use

--version: Displays version information and exits.

-h, --help: Displays usage information and exits.

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Code for computing various support scores for internodes

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