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A package for estimating phylogenetic tree for epigenomes (DNA methylation primarily) from multiple species.

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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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