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Burntrees

Perl script for printing and manipulating output from phylogenetic MCMC programs.

Currently, the script will handle tree- and parameters files from MrBayes (.t, .con, .p), BEAST/BEAST2 (.trees, .log), and PhyloBayes (.trace, .treelist).

The script may also be able to handle other Newick- or Nexus-formatted tree files.

For usage and examples, please see the Documentation below.

Files:

  • burntrees.pl -- main script
  • catmb.pl -- helper script for concatenating files using burntrees.pl. In order for catmb.pl to work, burntrees.pl must be installed in the PATH. Alternatively, the full path to burntrees.pl can be specified by editing catmb.pl.
  • data.t, data.p -- test data

Documentation

NAME

burntrees.pl

VERSION

Documentation for burntrees.pl version 0.3.1

SYNOPSIS

burntrees.pl [--burnin=<number>] [--pburnin=<number>] [--start=<number>]
[--end=<number>] [--jump=<number>] [--IFeelLucky=<number>] [--treesonly]
[--rmbrlens] [--rmcomments] [--rmsupport] [-R] [--sci2norm=<nr>]
[--seed=<nr>] [--myr] [--[no]close] [--getinfo] [--[no]labels]
[--format=altnexus|phylip] [--outfile=<file_name>] FILE [> OUTPUT]

DESCRIPTION

Script for manipulating tree (.t, .trprobs, .con, .trees) and parameter (.p, .log) files from MrBayes (v.3), BEAST, and PhyloBayes.

The script extracts trees and (by default) the taxon translation table and the trailing "end;" from tree file.

A number of options are available:

Any contiguous interval of trees can be printed, as well as trees only (nothing other than tree descriptions).

The samples can be thinned by setting a value for how many trees to jump before next is printed.

Branch lengths, support values, and comments can be removed from trees before printing.

Branch lengths in scientific numeric format can be transformed to a fixed numeric format.

MrBayes clock trees with branch lengths in substitutions per site can be transformed to branch lengths in time units.

A random set of trees can be printed from the tree file.

Lines can also be extracted from a MrBayes .p file.

Trees can be printed in Phylip (Newick) format or as altnexus (sequence labels instead of numbers), that is, the script can serve as an efficient tree format converter.

OPTIONS

Mandatory arguments to long options are mandatory for short options too

-b, --burnin=*number*
        Start printing after tree *number*.

-c, --close
        Forces a trailing "end;" to be printed after the last tree.
        --noclose prevents the "end;" to be printed. Note that the
        trailing "end;" in the tree file is printed by default unless
        --noclose is given.

-co, --concatenate
        Concatenate several files -- *Not yet implemented*. See USAGE
        for alternatives.

-e, --end=*number*
        End the printing of trees after tree *number* (inclusively). If
        no --end is given, prints to last tree in file.

-f, --format=*format*
        Trees are printed as specified by *format*, where *format* is
        either *altnexus*: with sequence (taxon) labels instead of
        numbers, or *phylip* (the Newick format).

-g, --getinfo
        Print information about the number of trees (or samples in p
        file), thinning, number of samples, presence of branch lengths
        and support values in file and quit.

-h, --help
        Prints help message and exits.

-i, --IFeelLucky=*number*
        Specify a probability (value between 0 -- 1) for each tree to be
        printed. That is, print each tree with prob. *number*. The -i
        option can be combined with the option -seed to create
        reproducible results. Note that --IFeelLucky has precedence over
        --jump.

-j, --jump=*number*
        Specify a thinning. That is, print every *number* tree.

-l, --labels
        Print trees using sequence (taxon) labels instead of the
        sequence numbers from the translation table. --nolabels (which
        is the default) prevents the sequence numbers to be substituted.

-ma, --man
        Displays the manual page.

-my, --myr
        Transform branch lengths in a MrBayes clock tree from
        substitutions per site to time units.

-o, --outfile=*file_name*
        Print directly to file *file_name* instead of standard out.

-p, --pburnin=*number*
        Start printing after a fraction of the run, where *number* is a
        percentage (e.g. "50" for half the run).

-rmb, --rmbrlens
        Remove branch lengths from trees.

-rmc, --rmcomments
        Remove comments (text within, and the enclosing square brackets)
        from trees.

-rms, --rmsupport
        Remove support values (bootstrap/posterior probabilities) from
        trees.

-R      Remove branch lengths, comments, and support values.

-sc, --sci2norm=*number*
        Translate branch lengths from scientific to normal or fixed.
        Change the precision by specifying the (optimal) *number*.

-se, --seed=*number*
        Set a seed for the *-i* option to create reproducible sampling
        results.

-st, --start=*number*
        Start printing from tree *number* (inclusively).

-t, --treesonly
        Print trees only (do not print taxon descriptions etc.). If used
        on a *.p file it skips the "ID" line and the headers.

-v, --version
        Prints version message and exits.

FILE    Reads a Nexus formatted tree FILE, preferrably MrBayes (v.3)
        *.t, *.con, and *.trprobs files. FILE can also be a MrBayes
        parameter file (*.p), or any Nexus formatted tree file, e.g.,
        output from BEAST or other phylogenetic MCMC software (not
        thoroughly tested!).

OUTPUT  Prints to STDOUT unless --outfile= is used.

USAGE

Examples:

  burntrees.pl --burnin=10 data.t > out.t
  burntrees.pl --pburnin=50 data.t
  burntrees.pl --start=11 --end=30 data.t
  burntrees.pl --jump=10 data.t
  burntrees.pl --treesonly data.t
  burntrees.pl --getinfo -b=10 data.t
  burntrees.pl --rmbrlens data.t
  burntrees.pl --rmcomments data.t
  burntrees.pl --ifeellucky=0.50 data.t
  burntrees.pl -b=10 -j=10 -t -rmb data.t
  burntrees.pl --treesonly -b=10 data.p
  burntrees.pl --format=altnexus data.t
  burntrees.pl -f=phylip --outfile=data.phy data.t
  burntrees.pl -f=p -b=1 data.con.tre

For concatenation of several files, use (note the append redirection, ">>". See also separate script catmb.pl):

  burntrees.pl -b=10 -noc  data.run1.t >  data.t
  burntrees.pl -b=40 -t    data.run2.t >> data.t
  burntrees.pl -b=20 -t -c data.run3.t >> data.t

To print the '#NEXUS', 'begin trees;', and the translation table only (no trees), or to print the header in .p, .trace, or .log files, use

  burntrees.pl -i -noc data.t

To convert a MrBayes file to a 'altnexus' file or a 'phylip' file, use

  burntrees.pl --format=altnexus data.t
  burntrees.pl --format=phylip data.t

To concatenate several files in to one altnexus formatted file, use (note the combination of '--format' and '--labels')

  burntrees.pl -b=10 -noc  -f=a data.run1.t >  data.t
  burntrees.pl -b=40 -t    -l   data.run2.t >> data.t
  burntrees.pl -b=20 -t -c -l   data.run3.t >> data.t

To extract the 10th tree in phylip format, use

  burntrees.pl --start=10 --end=10 --format=phylip data.t

To extract the second tree in the MrBayes .con.tre file (simple format) in phylip format, use

  burntrees.pl -b=1 -f=p data.con.tre

To remove comments from tree descriptions (e.g. trees in "figtree" format), use

  burntrees.pl --rmcomments data.con.tre

To remove support values from tree description for the first tree in a MrBayes .con.tre file (simple format) while changng branch lengths from scientific to normal (three decimals), use

  burntrees.pl --start=1 --end=1 --rmsupport --sci2norm=3 data.con.tre

To remove branch lengths from tree descriptions, use

  burntrees.pl --rmbrlens data.t

To remove branch lengths, support values, and comments from tree descriptions, use

  burntrees.pl -R data.t

To change the branch length format from scientific to numerical (three decimals) use

  burntrees.pl --sci2norm=3 data.con.tre

To change the MrBayes clock branch length format from substitutions per site to time units (Myr) use

  burntrees.pl --myr clock.t
  burntrees.pl --myr --rmcomments clock.t

To (randomly) sample a specific number of trees, use burntrees.pl together with 'shuf'. Note that you could sample more trees than you have in your tree file (i.e., performing a bootstrap)!

  burntrees.pl -t data.t | shuf -rn 10
  burntrees.pl -t -f p data.t | shuf -rn 1000

AUTHOR

Written by Johan A. A. Nylander

REPORTING BUGS

Please report any bugs to Johan.Nylander @ nbis.se.

DEPENDENCIES

Uses Perl modules Getopt::Long and Pod::Usage

DOWNLOAD

https://github.com/nylander/Burntrees

LICENSE AND COPYRIGHT

Copyright (c) 2006-2020 Johan Nylander

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.


NAME

catmb.pl

VERSION

Documentation for catmb.pl version 0.1.2

SYNOPSIS

catmb.pl [--burnin=<number>] [--pburnin=<number>] [--jump=<number>]
FILE FILE [...] [> OUTPUT]

DESCRIPTION

Script for manipulating tree (.t) and parameter (.p) files from MrBayes (v.3). This script is a helper for concatenating several files in to one (using the same burnin) using the script 'burntrees.pl'. burntrees.pl needs to be installed for catmb.pl to work.

OPTIONS

Mandatory arguments to long options are mandatory for short options too

-b, --burnin=*number*
        Start printing after tree *number*.

-p, --pburnin=*number*
        Start printing after a fraction of the run, where *number* is a
        percentage (e.g. "50" for half the run).

-j, --jump=*number*
        Specify a thinning. That is, print every *number* tree.

FILE    Reads Nexus formatted tree FILEs, preferrably a MrBayes (v.3)
        *.t file. Can also read and print a MrBayes parameter file (*.p
        file).

OUTPUT  Prints to STDOUT.

-h, --help
        Prints help message and exits

-v, --version
        Prints version message and exits

-m, --man
        Displays the manual page

USAGE

Examples:

  catmb.pl --burnin=10 run1.t run2.t run3.t > out.t
  catmb.pl --pburnin=50 run1.t run2.t run3.t > out.t
  catmb.pl --jump=10 run1.t run2.t run3.t > out.t

AUTHOR

Written by Johan A. A. Nylander

REPORTING BUGS

Please report any bugs to Johan.Nylander @ nrm.se.

DEPENDENCIES

Needs burntrees.pl to run. Uses Perl modules Getopt::Long and Pod::Usage

DOWNLOAD

https://github.com/nylander/Burntrees

LICENSE AND COPYRIGHT

Copyright (c) 2006-2020 Johan Nylander

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

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Perl scripts for manipulating output from phylogenetic MCMC software (MrBayes, BEAST, PhyloBayes, etc)

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