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

longbow0 / Burntrees