To compile this code, download it, unzip it, and run the following from the top-level directory of the unzipped code:

```bash
conda create -n qt qt
conda activate qt

qmake
make

mkdir bin
cp col*xml clustalx.hlp bin/
cp clustalx.app/Contents/MacOS/clustalx bin/

install_name_tool -change @rpath/libQt5Widgets.5.dylib $CONDA_PREFIX/lib/libQt5Widgets.5.dylib bin/clustalx
install_name_tool -change @rpath/libQt5Gui.5.dylib $CONDA_PREFIX/lib/libQt5Gui.5.dylib bin/clustalx
install_name_tool -change @rpath/libQt5Xml.5.dylib $CONDA_PREFIX/lib/libQt5Xml.5.dylib bin/clustalx
install_name_tool -change @rpath/libQt5Core.5.dylib $CONDA_PREFIX/lib/libQt5Core.5.dylib bin/clustalx
```

Finally, to run the code, just run `bin/clustalx`.


# Changes relative to official release

I just ran these commands to update for Qt 5:

```bash
sed -i '' 's/include <QtGui>/include <QtWidgets>/g' *.cpp
sed -i '' 's/toAscii/toLatin1/g' *.cpp
sed -i '' $'s/#include <stdexcept>/#include <string>\\\n#include <stdexcept>/g' clustalW/general/VectorOutOfRange.h
sed -i '' 's/QT += xml/QT += xml widgets/g' clustalx.pro
```


# Old README

Please see also ftp://ftp.ebi.ac.uk/pub/software/clustalw2/README

HOWTO COMPILE THE SOURCE AND INSTALL
----------------------------------------------------------------------

You will need a Unix environment with a working C++ compiler  and the
Qt developer kit (>=version 4.3) to compile the ClustalX source.

For compilation under Windows you will also need to install mingw and
cygwin.

Type
$ qmake
and then
$ make
This will create the clustalX binary.


HOWTO INSTALL AFTER COMPILATION
----------------------------------------------------------------------

Put colprot.xml, coldna.xml, colprint.xml, clustalx.hlp and
clustalX[.exe] into one folder. Add a link to the binary to your Desktop for
example.

On Linux you can use the installer script.