Filo 1.1 – Simulate Sequence Data used in Phylogenetic Analyses

Filo 1.1


Filo is designed to be used to simulate (molecular) sequence data used in phylogenetic analyses under very general conditions, including:

  • insertions and deletions; Insertions and deletions are propagated through the tree so the output file can be made to be the “true” alignment. This is very handy for checking out alignment methods, and is one of the main motivations for writing this program.
  • different phylogenetic histories (trees) along a sequence;
  • arbitrary rate matrices for each tree;
  • definition and re-use of node, branch, tree and global parameters;
  • output in various formats for subsequent analysis, e.g. in phylogenetic inference programs;
  • generation of trees under standard models such as Yule and All Trees Equally Likely.


Dr. Michael Charleston




  • Linux / Windows / MacOsX
  • Java




This software is intended for use in generating simulated sequence data for phylogenetic analysis. It is released as is, and with no warranty of any kind. Use it at your own risk!

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