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.

Output files

Description of BAMBE output files.

File	Description
file-root.lpd	stores the log of the unnormalized posterior density at each sample point
file-root.par	stores parameter values at each sample point
file-root.top	stores the tree topology at each sample point
file-root.out	stores the run characteristics and several data summaries
file-root.tre	which stores the final tree

More details:

• file-root.par has on each line in this order:
  • cycle number
  • log likelihood
  • tree acceptance proportion in most recent sample-interval cycles
  • parameter acceptance proportion in most recent sample-interval cycles
  • tree height (molecular clock) or half tree diameter (non-clock model)
  • global tuning parameter
  • eight parameters for each site-category
    • theta
    • kappa
    • ttp
    • gamma
    • pi_A
    • pi_G
    • pi_C
    • pi_T
• file-root.out contains sections:
  • Data summary with:
    • number of taxa
    • total number of sites
    • total number of unique sites. Two identical sites in different categories are considered to be different. The symbols `-', `N', `X', and `?' are all identical for this purpose.
  • Constant site information by category.
  • Overall appearance of each symbol. (The symbols `-', `N', `X', and `?' are all identical for this purpose.)
  • Appearance of each symbol by category and initial pi values from observed frequencies.
  • Frequency of bases by taxon.
  • Taxon names.
  • Run settings.

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