Epiphyte

Epiphyte is a software package for estimating phylogenetic tree from epigenetic modification (DNA methylation primarily) profiles of multiple species. It assumes

• known phylogenetic relationship between species
• epigenetic modification has binary state

Download

In a terminal, type

git clone --recursive https://github.com/smithlabcode/Epiphyte.git

Because Epiphyte depends on methpipe, if you haven't downloaded methpipe package, please also type

git clone --recursive https://github.com/smithlabcode/methpipe.git

Installation

Before attempting to compile Epiphyte please make sure:

• GNU Scientific Library (http://www.gnu.org/software/gsl/) is installed on your system.
• Header-only Boost libraries (http://www.boost.org/) exist in the system under the default directory /usr/include. Otherwise, specify the customized location of boost in the environment variable BOOST_ROOT:

  export BOOST_ROOT=/path/to/boost_1_64_0
  

• path to Methpipe (https://github.com/smithlabcode/methpipe) is
  defined in the environment variable METHPIPE_ROOT:

  export METHPIPE_ROOT=/path/to/methpipe
  

To compile Epiphyte, enter the program's root directory (e.g. Epiphyte/) and execute

make && make install

After the compilation, the binaries can be found in Epiphyte/bin/

Usage

PROGRAM: indep-methprob

Compute posterior probability for hyper-methylation state assuming independent sites

Usage: indep-methprob [OPTIONS] <methcount>

Option	Long tag	Type	Default	Description
-o	-out	str	stdout	output file
	-params-in	str	null	parameters file (no training)
	-params-out	str	null	output estimated parameters
-v	-verbose	bool	false	print more run info (default)

To see the list of options, use "-?" or "-help"

PROGRAM: indep-epi-phylo

Estimate tree shape and mutation rates assuming independent sites

Usage: indep-epi-phylo [OPTIONS] <newick> <meth-tab>

Option	Long tag	Type	Default	Description
-p	-params	str	null	use given parameters and skip optimization
-i	-iteration	int	100	maximum number of iteration
-n	-nodemap	bool	false	output MAP states of individual nodes
-o	-out	str	stdout	output file
-v	-verbose	bool	false	print more run info

To see the list of options, use "-?" or "-help".

PROGRAM: epiphy-est

Estimate phylogeny shape and methylation state transition rates for methylome evolution

Usage: epiphy-est [OPTIONS] <newick> <methprob-tab> -o <out.params>

Option	Long tag	Type	Default	Description
-d	-desert	int	1000	desert size
-i	-maxiter	int	100	max EM iterations
-h	-mcmc-iter	int	500	max mcmc iterations
-c	-complete	bool	false	input is complete observations
-k	-keep	int	100	samples per chain
-b	-burn-in	int	100	burn-in
-f	-first-only	bool	false	only burn-in in first EM iteration
-r	-restart	bool	false	restart MCMC chain in each EM iteration
-s	-seed	int	null	rng seed
-v	-verbose	bool	false	print more run info
-o	-out	str	null	output file name

To see the list of options, use "-?" or "-help".

PROGRAM: epiphy-post

Estimate posterior methylation probabilities at ancestral and unobserved sites

Usage: epiphy-post [OPTIONS] <param-file> <methprob-table> -o <out.post>

Option	Long tag	Type	Default	Description
-o	-outfile	str	null	output file
-h	-mcmc-iter	int	100	max mcmc iterations
-b	-burn	int	1000	burnin size
-c	-complete	bool	false	input is complete observations, only compute likelihood
-d	-desert	int	1000	desert size (default:1000)
-m	-mark	bool	false	mark sites for posterior estimation
-v	-verbose	bool	false	print more run info
-s	-seed	int	null	rng seed

Copyright

Copyright (C) 2015 University of Southern California Andrew D. Smith

Authors: Jianghan Qu and Andrew D. Smith

EPIPHYTE is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

EPIPHYTE is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with EPIPHYTE. If not, see http://www.gnu.org/licenses/.

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