Note Phyx recently overwent an overhaul such that a simple git pull && git make will fail. Instead, see instructions here.

phyx performs phylogenetics analyses on trees and sequences. See installation instructions for Linux and Mac including any dependencies on the wiki here or below.

Authors: Joseph W. Brown*, Joseph F. Walker*, and Stephen A. Smith (* equal contribution)

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

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

Some of the sequence comparison operations use the very nice edlib library. 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.

Documentation

Documentation resides in several locations (all slightly out of date, alas). A pdf manual is available in the doc/ directory. A slightly-less-out-of-date list of the current programs with examples can be found on the wiki. Help for individual programs can be obtained with either PROGRAM -h or (if installed, see below) man PROGRAM. See a brief overview here.

Still, there are a whack of programs, so it can be difficult to remember the name of which program does what. Here is a quick reference:

Program	Short description
pxaa2cdn	produce a codon alignment from and AA alignment and unaligned nucleotides
pxbdfit	diversification model inference
pxbdsim	a birth death simulator
pxboot	sequence alignment resampling (bootstrap or jackknife)
pxbp	prints out bipartitions that make up the tree
pxcat	an alignment concatenator
pxclsq	clean sites based on missing or ambiguous data
pxcltr	general tree cleaner
pxcolt	collapse poorly-supported edges
pxcomp	a composition homogeneity test
pxcomp	compositional homogeneity test
pxconsq	a consensus sequence constructor for an alignment
pxcontrates	a brownian and ou estimator
pxfqfilt	a fastq filter given a mean quality
pxlog	a MCMC log manipulator/concatenator
pxlssq	information about seqs in a file (like ls but for an alignment file)
pxlstr	information about trees in a file (like ls but for a tree file)
pxmono	monophyly tester
pxmrca	information about an mrca
pxmrcacut	a mrca cutter
pxmrcaname	a mrca label maker
pxnj	neighbour-joining tree inference
pxnni	a nni changer
pxnw	needleman-wunsch alignment
pxpoly	a polytomy sampler that generates a binary tree
pxrecode	a sequence alignment recoder
pxrevcomp	a reverse complementor
pxrls	taxon relabelling for sequences
pxrlt	taxon relabelling for trees
pxrmk	remove two-degree nodes from a tree
pxrms	pruning seqs (like rm but for seqs)
pxrmt	pruning trees (like rm but for trees)
pxrr	rerooting and unrooting trees
pxs2fa	convert an alignment to fasta format
pxs2nex	convert an alignment to nexus format
pxs2phy	convert an alignment to phylip format
pxseqgen	sequence simulation program
pxssort	sequence sorter
pxssplit	split alignment into N individual sequence files
pxsstat	multinomial alignment test statistics
pxstrec	a state reconstructor
pxsw	smith waterman alignment
pxt2new	convert a tree to newick format
pxt2nex	convert a tree to vanilla Nexus format
pxtcol	annotate tree to colour edges
pxtcomb	tree combiner
pxtgen	exhaustive tree topology generator
pxtlate	translate nucleotide sequences into amino acids
pxtrt	extract an induced subtree from a larger tree
pxtscale	tree rescaling
pxupgma	upgma tree inference
pxvcf2fa	convert vcf file to fasta alignment

Problems after updating (git pull)

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
make check
sudo make install

Installation instructions

phyx requires a few dependencies. Since installation of these dependencies differs on Linux vs. Mac OSX, 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 or using a fresh installation of gcc from here. Instructions for both are below (don't use both, choose one, probably the simple one). For simple instructions click here, and for advanced instructions click here.

Binary install with Homebrew

Install the Homebrew package manager:

 /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

Install the Brewsci phyx package:
```
 brew install brewsci/bio/phyx
```

Build from source with Homebrew

Install the Homebrew package manager:

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

Install dependencies from homebrew:

 brew install git cmake nlopt armadillo

On to phyx. First, clone the repository (if you haven't already):
```
 git clone https://github.com/FePhyFoFum/phyx.git
```

Install phyx

 cd phyx/src
 autoconf
 ./configure
 make
 make check

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

    sudo make install

Install with HPC GCC (advanced instructions)

Install gcc and gfortran. Download gcc-6.2-bin.tar.gz or more recent from http://hpc.sourceforge.net/. Install with:
```
 sudo tar -xvf gcc-6.2-bin.tar -C /
```

Install autoconf from http://ftp.gnu.org/gnu/autoconf/. Get autoconf-latest.tar.gz, then:

 tar -xzf autoconf-latest.tar.gz
 cd autoconf-2.69
 ./configure --prefix=/usr/local/autoconf-2.69
 make
 sudo make install
 ln -s autoconf-2.69 /usr/local/autoconf

On to phyx. first, clone the repository (if you haven't already):
```
 git clone https://github.com/FePhyFoFum/phyx.git
```
Install cmake and install Armadillo. Get cmake from https://cmake.org/download/. I got https://cmake.org/files/v3.6/cmake-3.6.2-Darwin-x86_64.tar.gz. Get armadillo from the deps directory or http://arma.sourceforge.net/download.html, get the stable one. Untar it. Double click the Cmake.app. Click "Browse source..." and choose the armadillo folder that was created after untaring. Click "Browse build..." and choose the same folder as browse source. Click "Configure" and then click "Generate". Go to the terminal and browse to that armadillo folder and type:
```
 make
 sudo make install
```
Install nlopt. Get nlopt 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 --without-octave --without-matlab
 make
 sudo make install
```
Compile phyx. Now you can go to the src directory of phyx and type:
```
 autoconf
 ./configure
 make
 make check
 sudo make install
```

and all the programs should compile without issue.

Linux install

These instructions work for most ubuntu versions as well as debian.

Install general dependencies:

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

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

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

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
    tar -xvzf armadillo-7.400.2.tgz
    cd armadillo-7.400.2
    ./configure
    make
    sudo make install

Finally, install phyx:

 cd phyx/src
 autoconf
 ./configure
 make
 make check

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

    sudo make install