Skip to content
Perl scripts for manipulating output from phylogenetic MCMC software (MrBayes, BEAST, PhyloBayes, etc)
Perl HTML OpenEdge ABL
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
.gitignore
README.md
burntrees.html
burntrees.pl
burntrees.txt
catmb.html
catmb.pl
catmb.txt
data.p
data.t

README.md

Burntrees

Perl script for printing and manipulating MrBayes tree files (.t, .con), MrBayes parameter files (.p), or other Nexus-formatted tree files. Also tested with output from BEAST/BEAST2 (.trees, .log), and PhyloBayes (.trace, .treelist).

Written by:

Johan Nylander

Examples

(See documentaion for more)

  • Burnin 10 trees

      burntrees.pl --burnin=10 data.t > out.t
    
  • Burnin 50%

      burntrees.pl --pburnin=50 data.t
    
  • Get trees 11 to 30

      burntrees.pl --start=11 --end=30 data.t
    
  • Thin by sampling every 10th tree

      burntrees.pl --jump=10 data.t
    
  • Get trees only

      burntrees.pl --treesonly data.t
    
  • Get info on samples (after the burnin of 10)

      burntrees.pl --getinfo -b=10 data.t
    
  • Remove branch lengths from trees

      burntrees.pl --rmbrlens data.t
    
  • Remove comments from trees

      burntrees.pl --rmcomments data.t
    
  • Sample every tree with prob 0.5

      burntrees.pl --ifeellucky=0.50 data.t
    
  • Burnin 10, thin by 10, trees only, remove branch lengths

      burntrees.pl -b=10 -j=10 -t -rmb data.t
    
  • Burnin 10 from a parameter file

      burntrees.pl -b=10 data.p
    
  • Burnin 10, remove headers from a parameter file

      burntrees.pl --treesonly -b=10 data.p
    
  • Convert trees to altnexus format

      burntrees.pl --format=altnexus data.t
    
  • Convert trees to Phylip (Newick) format, save to file

      burntrees.pl -f=phylip --outfile=data.phy data.t
    
  • Get second tree from MrBayes .con.tre file in Phylip format

      burntrees.pl -f=p -b=1 data.con.tre
    
  • Change branch length format from scientific to numerical (three decimals)

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

Files:

  • burntrees.pl -- the Perl script

  • burntrees.txt -- documentation in text format

  • burntrees.html -- documentation in html format

  • catmb.pl -- Perl script for concatenating files using burntrees.pl

  • catmb.txt -- documentation in text format

  • catmb.html -- documentation in html format

  • data.t, data.p -- test data

Get started

Make sure the file burntrees.pl is executable (chmod +x burntrees.pl) and

./burntrees.pl

CatMB

Perl script for concatenating several MCMC runs.

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. (Then chmod +x catmb.pl) and

./catmb.pl
You can’t perform that action at this time.