New upstream version 0.999+ds

CMakeLists.txt

convert_phylip_to_states.py

logo.svg

*.bbl

*.blg

*.synctex.gz

Phyxed_Manual.log

Phyxed_Manual.dvi

Authors: Joseph W. Brown, Joseph F. Walker, and Stephen A. Smith

Citation: [Brown, J. W., J. F. Walker, and S. A. Smith; Phyx: phylogenetic tools for unix. Bioinformatics 2017; 33 (12): 1886-1888. doi: 10.1093/bioinformatics/btx063](https://academic.oup.com/bioinformatics/article/33/12/1886/2975328/Phyx-phylogenetic-tools-for-unix)

License: GPL https://www.gnu.org/licenses/gpl-3.0.html

Some of the sequence comparison operations use the very nice [edlib library](https://github.com/Martinsos/edlib#alignment-methods). These are reported in this publication: [Martin Šošić, Mile Šikić; Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance. Bioinformatics 2017 btw753. doi: 10.1093/bioinformatics/btw753](https://academic.oup.com/bioinformatics/article/33/9/1394/2964763/Edlib-a-C-C-library-for-fast-exact-sequence).

## Update 31 May 2018

If you have been using phyx and things are not working after a recent pull, this is because of a change in configuration. Please do the following in the `src` directory to remedy the situation:

    make distclean

    autoreconf -fi

    ./configure

    make

    sudo make install

# Installation instructions 

phyx requires a few dependencies. Since installation of these dependencies differs on [Linux](#linux-install) vs. [Mac OSX](#mac-install), we've separated the instructions below. 

## Mac install

Mac has become increasingly difficult to support at the command line with changes every version on location and standards for compilation tools. First, distribution of compiled programs is very difficult. Furthermore, Mac now defaults to clang as a C/C++ compiler, which does not support OpenMP.  For **Mac OSX 10.12**, we have found that you can install with clang using the simple instructions and [homebrew] (http://brew.sh/) *or* using a fresh installation of gcc from [here](http://hpc.sourceforge.net/). Instructions for both are below (don't use both, choose one, probably the simple one). For simple instructions click [here](#install-with-homebrew-simple-instructions), and for advanced instructions click [here](#install-with-hpc-gcc-advanced-instructions).

Mac has become increasingly difficult to support at the command line with changes every version on location and standards for compilation tools. First, distribution of compiled programs is very difficult. Furthermore, Mac now defaults to clang as a C/C++ compiler, which does not support OpenMP.  For **Mac OSX 10.12**, we have found that you can install with clang using the simple instructions and [homebrew] (http://brew.sh/) *or* using a fresh installation of gcc from [here](http://hpc.sourceforge.net/). Instructions for both are below (don't use both, choose one, probably the simple one). For simple instructions click [here](#binary-install-with-homebrew), and for advanced instructions click [here](#install-with-hpc-gcc-advanced-instructions).

### Install with Homebrew (simple instructions)

The instructions below assume homebrew, which is convenient for dealing with dependencies.

### Binary install with Homebrew

1. Install the homebrew package manager:

1. Install the Homebrew package manager:

        /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

2. Install the Brewsci phyx package:

        brew install brewsci/bio/phyx

### Build from source with Homebrew

1. Install the Homebrew package manager:

        /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

2. Install dependencies from homebrew:

        brew install git

        brew install cmake

        brew install homebrew/science/nlopt

        brew install git cmake nlopt armadillo

3. On to phyx. first, clone the repository (if you haven't already):

        git clone https://github.com/FePhyFoFum/phyx.git

4. Install the final dependency, armadillo, (included with phyx):

		cd phyx/deps

		tar -xzf armadillo-7.400.2.tgz

		cd armadillo-7.400.2

		./configure

		make

		sudo make install

5. Install phyx

4. Install phyx

		cd ../../src

        cd phyx/src

        ./configure

        make

        python run_tests.py

5. Install nlopt. Get armadillo from the `deps` directory or go to http://ab-initio.mit.edu/wiki/index.php/NLopt#Download_and_installation and download the latest (probably nlopt-2.4.2.tar.gz). Untar and browse in the terminal to that directory:

        ./configure --with-cxx --without-octave --without-matlab

        ./configure --without-octave --without-matlab

        make

        sudo make install

1. Install general dependencies:

        sudo apt-get install git

        sudo apt-get install autotools-dev

        sudo apt-get install autoconf

        sudo apt-get install automake

        sudo apt-get install cmake

        sudo apt-get install libtool

        sudo apt-get install liblapack-dev

        sudo apt-get install libatlas-cpp-0.6-dev

        sudo apt-get install git autotools-dev autoconf automake cmake libtool liblapack-dev libatlas-cpp-0.6-dev libnlopt-dev libnlopt0

2. Clone the phyx repo (if you haven't already):

        git clone https://github.com/FePhyFoFum/phyx.git

3. Install nlopt dependency (default is C, we need C++; not available from apt-get):

        cd phyx/deps

        tar -xvzf nlopt-2.4.2.tar.gz

        cd nlopt-2.4.2

        ./configure --with-cxx --without-octave --without-matlab

        make

        sudo make install

4. Install armadillo dependency  

3. Install armadillo dependency  

**Note**: it is possible to get from apt-get, but need version >= 5.2:

        sudo apt-get install libarmadillo-dev

On debian it was necessary to use backports:

        sudo apt-get -t jessie-backports install libarmadillo-dev

If that is not possible, compile the provided code:

        cd phyx/deps

        ./configure

        make

        sudo make install

5. Finally, install phyx:

4. Finally, install phyx:

        cd phyx/src

        ./configure

        make

        python run_tests.py

If you want to install it so it is available anywhere in your system, do:

        sudo make install

\newlabel{abstract}{{\M@TitleReference {}{What is Phyx?}}{1}{What is Phyx?}{section*.1}{}}

\@writefile{toc}{\contentsline {subsection}{Installing Phyx}{1}{section*.2}}

\newlabel{introduction}{{\M@TitleReference {}{Installing Phyx}}{1}{Installing Phyx}{section*.2}{}}

\@writefile{toc}{\contentsline {section}{Features of Phyx}{1}{section*.3}}

\@writefile{toc}{\contentsline {section}{Pheatures of Phyx}{1}{section*.3}}

\@writefile{toc}{\contentsline {subsection}{Data formats}{1}{section*.4}}

\@writefile{toc}{\contentsline {subsection}{Repeatability}{2}{section*.5}}

\@writefile{toc}{\contentsline {subsection}{Piping}{2}{section*.6}}

\@writefile{toc}{\contentsline {subsection}{pxrr}{8}{section*.32}}

\@writefile{toc}{\contentsline {subsection}{pxs2fa and pxs2phy and pxs2nex}{8}{section*.33}}

\@writefile{toc}{\contentsline {subsection}{pxseqgen}{8}{section*.34}}

\@writefile{toc}{\contentsline {subsection}{pxstrec}{9}{section*.35}}

\@writefile{toc}{\contentsline {subsection}{pxsw}{9}{section*.36}}

\@writefile{toc}{\contentsline {subsection}{pxt2new}{9}{section*.37}}

\@writefile{toc}{\contentsline {subsection}{pxtlate}{10}{section*.38}}

\@writefile{toc}{\contentsline {subsection}{pxtscale}{10}{section*.39}}

\@writefile{toc}{\contentsline {subsection}{pxupgma}{10}{section*.40}}

\@writefile{toc}{\contentsline {subsection}{pxvcf2fa}{10}{section*.41}}

\@writefile{toc}{\contentsline {subsection}{pxsstat}{9}{section*.35}}

\@writefile{toc}{\contentsline {subsection}{pxstrec}{9}{section*.36}}

\@writefile{toc}{\contentsline {subsection}{pxsw}{9}{section*.37}}

\@writefile{toc}{\contentsline {subsection}{pxt2new}{10}{section*.38}}

\@writefile{toc}{\contentsline {subsection}{pxtlate}{10}{section*.39}}

\@writefile{toc}{\contentsline {subsection}{pxtscale}{10}{section*.40}}

\@writefile{toc}{\contentsline {subsection}{pxupgma}{10}{section*.41}}

\@writefile{toc}{\contentsline {subsection}{pxvcf2fa}{10}{section*.42}}

\memsetcounter{lastsheet}{10}

\memsetcounter{lastpage}{10}

\BOOKMARK [1][-]{section*.1}{What is Phyx?}{}% 1

\BOOKMARK [1][-]{section*.3}{Features of Phyx}{}% 2

\BOOKMARK [1][-]{section*.3}{Pheatures of Phyx}{}% 2

\BOOKMARK [1][-]{section*.7}{Examples}{}% 3