https://github.com/pblischak/qcf
Quartet concordance factor estimation
https://github.com/pblischak/qcf
Last synced: 22 days ago
JSON representation
Quartet concordance factor estimation
- Host: GitHub
- URL: https://github.com/pblischak/qcf
- Owner: pblischak
- License: gpl-3.0
- Created: 2018-02-27T16:19:28.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2020-02-06T19:55:02.000Z (over 5 years ago)
- Last Synced: 2025-05-15T02:11:59.539Z (22 days ago)
- Language: C++
- Homepage: http://qcf.readthedocs.io/
- Size: 218 KB
- Stars: 3
- Watchers: 1
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.rst
- Changelog: CHANGELOG.md
- License: LICENSE.rst
Awesome Lists containing this project
README
|Build Status| |Documentation| |QCF Version|
``qcf``: estimating quartet concordance factors
===============================================
`Read the Docs `__
==============================================
Installation
~~~~~~~~~~~~
``qcf`` can be installed by cloning this repo and then compiling the main executable
using the provided ``Makefile`` (see code below). ``qcf`` is written in C++ for Unix-like
operating systems and makes use of features from the C++11 standard, which
requires a compatible compiler (GNU ``g++`` >= 4.8, Clang ``clang++`` >= 3.3).
Mac users will also need to have the Xcode
`Command Line Tools `__ installed.
The software also comes with several Python scripts for processing and analyzing output.
These scripts have been tested on Python versions 3.5-3.7, and require the ``numpy``
package, which can be installed as follows: ``pip install numpy``.
The steps to compile, test, and install ``qcf`` and the associated scripts
is given here:
.. code:: bash
# Code to compile and install qcf
git clone https://github.com/pblischak/QCF.git # 1. Clone the repo from GitHub
cd QCF # 2. cd into the QCF/ folder
make # 3. compile the qcf executable
make test # 4. test that the executable
# and Python scripts are working
sudo make install # 5. copy executable and Python scripts
# to /usr/local/bin
Usage
~~~~~
After compiling and installing the software, you can use the program in a terminal
window by typing ``qcf``. Below are the main commands that can be used to estimate
quartet concordance factors using ``qcf``. More details on input data formats, as well
as background on interpreting the output, can be found in the
`tutorial `__ on the ReadTheDocs site.
**Basic usage**:
.. code:: bash
# Run the data in the example folder
cd example
qcf -i genes.txt -m map.txt --prefix example
# Run with 100 bootstrap reps
qcf -i genes.txt -m mapt.txt -b 100 --prefix bootstrap
Raw quartet scores and confidence intervals
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
In additional to calculating the QCF values for each species quartet, we have also
provided an option to print the gene-level quartet information to file to perform
per-gene bootstrap resampling for the calculation of confidence intervals on the
the species-level QCF values. This can activated by running ``qcf`` with the
``--printRaw`` flag added:
.. code::
# Print out the raw gene-tree quartet information
cd example/
qcf -i genes.txt -m map.txt --printRaw --prefix example
This raw output can then be processed using the ``qcf_boot.py`` Python script,
which will conduct bootstrap resampling across genes. Options for combining
runs across different sets of genes are available as well
(see `tutorial `__).
Getting Help
~~~~~~~~~~~~
If you have questions about running ``qcf``, please feel free to use the gitter chatroom to get help:
|Gitter|
If you have a problem while running ``qcf``, and you think it may be a bug, please consider filing an issue:
|QCF Issues|
.. |Build Status| image:: https://travis-ci.org/pblischak/QCF.svg?branch=master
:target: https://travis-ci.org/pblischak/QCF
.. |Documentation| image:: http://readthedocs.org/projects/qcf/badge/?version=latest
:target: http://qcf.readthedocs.io
.. |Gitter| image:: https://badges.gitter.im/Join%20Chat.svg
:target: https://gitter.im/quartet-cf/Lobby
.. |QCF Issues| image:: https://img.shields.io/badge/qcf-issues-blue.svg
:target: https://github.com/pblischak/QCF/issues
.. |QCF Version| image:: https://img.shields.io/badge/qcf-v0.2.0a-orange.svg
:target: https://github.com/pblischak/QCF/releases/tag/0.2.0a