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)
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Documentation resides in several locations (all slightly out of date, alas).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 A slightly-less-out-of-date list of the current programs with examples can be found on the wiki.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 |
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
phyx requires a few dependencies. Since installation of these dependencies differs on Linux vs. Mac OSX, we've separated the instructions below.
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.
-
Install the Homebrew package manager:
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" -
Install the Brewsci phyx package:
brew install brewsci/bio/phyx
-
Install the Homebrew package manager:
/usr/bin/ruby -e "$(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 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
depsdirectory 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
depsdirectory 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.
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