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.
burntrees.pl-- main scriptcatmb.pl-- helper script for concatenating files usingburntrees.pl. In order forcatmb.plto work,burntrees.plmust be installed in the PATH. Alternatively, the full path toburntrees.plcan be specified by editingcatmb.pl.data.t,data.p-- test data
burntrees.pl
Documentation for burntrees.pl version 0.3.1
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]
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.
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.
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
Written by Johan A. A. Nylander
Please report any bugs to Johan.Nylander @ nbis.se.
Uses Perl modules Getopt::Long and Pod::Usage
https://github.com/nylander/Burntrees
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.
catmb.pl
Documentation for catmb.pl version 0.1.2
catmb.pl [--burnin=<number>] [--pburnin=<number>] [--jump=<number>]
FILE FILE [...] [> OUTPUT]
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.
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
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
Written by Johan A. A. Nylander
Please report any bugs to Johan.Nylander @ nrm.se.
Needs burntrees.pl to run. Uses Perl modules Getopt::Long and Pod::Usage
https://github.com/nylander/Burntrees
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.