Phylogenetic Trees Visualization
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README.md

README.md

Phylogenetic Trees Visualization

This is the code and documentation for the project I created in 2006 as a minor project.

Documentation

Please read README.md and project documentation.

Sequence Alignment

The sequence alignment and tree building is actually done using ClustalW. So first we need to build clustalw1.83.

Download it:

wget -c http://www.microextreme.net/software/clustalw1.83.UNIX.tar.gz.tar

Unzip it to a folder

tar zxf clustalw1.83.UNIX.tar.gz.tar
cd clustalw1.83
make

Now invoke the clustalw program:

    bin/clustalw

How to build the visualization tools?

On Fedora

$ sudo yum install SoQt-devel
$ cd path/to/phyloviz
[phyloviz] $ mkdir build
[phyloviz] $ cd build/
[phyloviz/build] $ cmake ../ -DCOIN3D_INCLUDE_DIRS=/usr/include/Coin2/

On Ubuntu 14.04

$ apt-get install cmake libsoqt-dev
$ cd path/to/source/
[phyloviz] $ mkdir build
[phyloviz] $ cd build/
[phyloviz/build] $ cmake ../
-- The C compiler identification is GNU 4.8.2
-- The CXX compiler identification is GNU 4.8.2
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.26") 
-- Looking for Q_WS_X11
-- Looking for Q_WS_X11 - found
-- Looking for Q_WS_WIN
-- Looking for Q_WS_WIN - not found
-- Looking for Q_WS_QWS
-- Looking for Q_WS_QWS - not found
-- Looking for Q_WS_MAC
-- Looking for Q_WS_MAC - not found
-- Found Qt4: /usr/bin/qmake (found version "4.8.6") 
-- Found Coin3D: /usr/lib/x86_64-linux-gnu/libCoin.so  
-- Configuring done
-- Generating done
-- Build files have been written to: /home/saleem/work/learn/mine/phyloviz/build
[phyloviz/build] $ make
Scanning dependencies of target ev-iv
[ 50%] Building CXX object CMakeFiles/ev-iv.dir/src/ev-iv/ev-iv.cc.o
Linking CXX executable ev-iv
[ 50%] Built target ev-iv
Scanning dependencies of target ph2iv
[100%] Building C object CMakeFiles/ph2iv.dir/src/ph2iv/ph2iv.c.o
Linking C executable ph2iv
[100%] Built target ph2iv

The two executables have been built by now:

[phyloviz/build] $ ls ph2iv ev-iv

Further details on using these tools is show in documentation file. Please refer that document for "Generation and Visualization of Phylogenetic Trees".

Sample Data and other software

You can find some sample data and other software at: http://tuxdna.in/files/bioinformatics/

Debugging

If you like to build debug the code using a debugger you may want to generate debug binaries:

$ cmake -DCMAKE_BUILD_TYPE=Debug ../