BAMBE

Bayesian Analysis in Molecular Biology and Evolution

Version 2.03 beta, January 2001

© Copyright 2000, 2001, Donald Simon & Bret Larget, Department of Mathematics and Computer Science, Duquesne University.

Tree file format

BAMBE recognizes two tree file formats, Newick format and BAMBE format. Newick format is the standard tree format used by PHYLIP, PAML, PAUP, and other phylogeny packages. BAMBE format is useful for debugging and resembles the internal data structure used in our software.

Here is a sample tree in Newick format: 

(((Taxon 1:0.112641,(Taxon 5:0.051682,Taxon 6:0.051682):0.060959):0.013183,
Taxon 3:0.125824):0.008005,(Taxon 2:0.119994,Taxon 4:0.119994):0.013835);
When BAMBE reads in a tree in Newick format, it expects the taxon names to agree with those in the data file and will exit with an error if these do not match.

In BAMBE format the tree is written with one row per node and the format is completely described by this example. 

 7 6
taxon node lchild rchild parent branchlen    height
   1     0     -1     -1      9  0.112641  0.133829
   2     1     -1     -1      6  0.119994  0.133829
   3     2     -1     -1      8  0.125824  0.133829
   4     3     -1     -1      6  0.119994  0.133829
   5     4     -1     -1     10  0.051682  0.133829
   6     5     -1     -1     10  0.051682  0.133829
   7     6      1      3      7  0.013835  0.013835
   8     7      8      6     -1  0.000000  0.000000
   9     8      9      2      7  0.008005  0.008005
  10     9      0     10      8  0.013183  0.021188
  11    10      4      5      9  0.060959  0.082147
log likelihood = -3516.625633
The first number of the first row, `7' in this example, is the node number of the root. The second number specifies the number of leaves in the tree. Leaves of the tree are given node numbers from 0 up to one less than the number of leaves. The order of the internal nodes is arbitrary. All branch lengths should be nonnegative. The value -1 is used for an empty node label. (Leaves have no children, the root has no parent.) The last line of the file is unnecessary. Only the child information and branch lengths are actually used by BAMBE when reading in a tree. The taxon numbers correspond to the species in the order of the data file.

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This page was most recently updated on January 19, 2001.

bambe@mathcs.duq.edu