smithlabcode/Epiphyte

Name: Epiphyte

Owner: Smith Lab

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

Created: 2017-05-29 22:29:28.0

Updated: 2018-03-26 20:52:15.0

Pushed: 2018-02-05 23:48:04.0

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Size: 753

Language: C++

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README

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

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

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

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:

  rt BOOST_ROOT=/path/to/boost_1_64_0
  

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

  rt 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 © 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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