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A tool to determine molecular diagnostic characters for species from sequences in fasta format
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README.rst

Fastachar

Fastachar is a graphical user interface that allows a simple comparison of two sets of DNA sequences. A typical working example is to have a selection of DNA sequences of different, but related species. These sequences are divided in a set A, which are thought to be a single taxon (species) and a set B, which is a collection of different taxa. Using the program, it can be established easily whether:

  • the DNA sequences in set A are all identical, and if not, list the differences for those positions in the DNA sequences.
  • set B has positions in the DNA that are different from those in set A, across all species in set B.

Fastachar takes as input the alignments stored in a single file of the fasta format. Fastachar is not a tool to align sequences. It is assumed that the sequences were previously aligned with different algorithms (e.g. MUSCLE) and the most reliable alignment was chosen.

Installation

Fastachar is written in Python3 and should run on all major platforms, including linux and windows. In order to run Fastachar a working copy of the python3 interpreter is required (including the tkinter windowing toolkit).

Linux

Usually python3 is included in most linux distributions. A simple test is to open a terminal and try to run python by:

$ python3

which should give you the python interpreter (including its version number). If it is verified that this works, test for the presence of the tkinter windowing toolkit:

>>> import tkinter

If this does not raise an exception, then you are all good and you can exit the interpreter (ctl-D). Otherwise you will need to install tkinter yourself, which is probably best done via your distribution's package manager.

Fastachar can be installed from pypi, using pip from the command line:

$ pip3 install fastachar

or from a tar-gzipped file downloaded from github FastaChar github repository <http://github.com/smerckel/fastachar>. After extracting the .tgz file and cd-ing into the newly created directory, you run:

$ python3 setup.py build && sudo python3 setup.py install && sudo python3 setup.py clean

Either installation method for Fastachar should take care of installing the dependencies (xlwt) correctly.

Windows

Usually python is not installed by default on a Windows computer and needs to be installed by the user. In this readme the official python distribution will be used, but other python packages exist and may work equally well, too.

To install Python3, visit https://www.python.org/downloads/windows/ and select the (latest) python3 version. (Do not select Python2 as this is not supported by Fastachar.) When downloading the Python3 distribution, make sure you select the proper version for your computer hardware:

  • Download Windows x86 executable installer for a 32 bit system
  • Download Windows x86-64 executable installer for a 64 bit system.

You can check from the control panel/system which version your computer is running on, when in doubt.

When, the file is downloaded, run it and follow the default installation (which includes pip and tkinter, which are both needed for successful operation of Fastachar). It is recommend however to check the box to add Python3 to the PATH environment variable.

Once Python3 is installed, Fastachar can be installed using pip. This requires a dos prompt (go to Start/search for programs and enter cmd, which should give an entry to the dos-command line. Type in the dos-prompt:

pip3 install fastachar

or:

py -3 pip -m install fastachar

which should also install the dependencies numpy and xlwt.

Alternatively, Fastachar can be installed using an MSI file, which can be downloaded from http://cubic-l.science/fastachar.html.

Authors

  • Lucas Merckelbach (lucas.merckelbach at hzg.de)
  • Luisa Borges (info at cubic-l.science or luisaborges2000 at yahoo.co.uk)

The software is released under the GPLv3 licence.

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