hj1994412/burntrees

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

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

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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