Category: Science-CAD
Filo
Download: http://www.it.usyd.edu.au/~mcharles/software/filo/filo.zip
Operation System: Windows All
License:
Size: 91 KB
Date: 2010-10-26 23:13:33
Filo is a command-line Java program that was 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. Filo can be run using either entirely command-line arguments or using input file(s). Using the command-line is a bit more restrictive because it just gets too awkward to write a huge great set of arguments when you can put them into an input file in a more easily read way. The input file uses a simple syntax that is consistent with the NEXUS format, and uses a "Filo" block. Filo can be used to run many simulations in batches. The input file can be thought of as a script of commands that are run in order. The idea is that you can define models to use very generally on any part of a tree, including branch lengths of course, and different matrices on each branch, different indel rates, and by combining trees with their own sets of parameters. The parameters are grouped into general, tree and branch parameters. General parameters- refer to those which apply across all the trees (overall rates, base frequencies, root-to-tip distances etc.), and govern simulation settings too, such as number of trials (e.g., number of trials, output format); Tree parameters- are those parameters which are to be assumed for agiven tree, identified by a label you choose. In general it makes sense to use the same label for a set of tree parameters as you chose for the tree itself. These parameters are such things as initial sequence length (which can change through the tree if there are insertions or deletions permitted), birth/death rate of lineages in the tree if the tree itself is to be grown through time, insertion/deletion parameters of rate and mean length, number of tips to which to grow, whether the molecular clock should be used, the initial base frequency, etc. The individual parameters are detailed later. Branch parameters- are a selection of those parameters above, which apply to a whole tree, and applied to a single branch identified by a label you choose. These are indel parameters, branch length, and the transition matrix used. Requirements:
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