Files
This page describes the files produced by TESD.
The
.para files
File of the simulation parameters.
- first line : Choose the simulation model
- "NM"
for the normal model
- "LB"
for the local burst model (not available in the present 1.0 version of TESD
- line 2 : Duration of the simulation
- line 3 : Number of populations (at least two)
- line 4 : Specify whether:
- the population sizes are homogeneous: "H"
- the population sizes are different between populations: "NH"
- line 5 : Specify the population sizes
- Populations are all equal in size: then type the size
as a unique integer
- Populations have different sizes: then specify the size of each population
- line 6 : Specify the number of transposable
element copies in each population
- line 7 : Specify whether:
- migration rates between populations are homogeneous: "H"
- migration rates between populations are different: "NH"
- line 8 : migrations:
- if migration rates between populations are homogeneous,
enter the number of migrating individuals (decimal accepted as migration rate can be considered as an average for some generations)
- if migration rates between populations are not homogeneous, then specify the migration rate values in a matrix. For example, with 3
populations:
- line 8 : 1.3 [pop 2 - pop 1]
- line 9 : 0.7 [pop 3 - pop 1] (tabulation) 2.01 [pop 3 -
pop 2]
The
.mea and .var files
These files contain, for each generation, the
mean and variance of the number of copies of transposable elements in each population as .mea and .var files.
The
.frq files
In TESD, each of the three chromosomes contains 120 possible sites of insertion of
transposable elements. The file shows the population frequency of the transposable
element insertions for each of these 360 sites.
The
.coo files
This file saves the specific coordinates assigned to each
population in a Map representation.
How
TESD manages files
Directories
The initial default directory is decided by your Java virtual machine
to be your document directory, depending on you Operating
System.
When you open a file from a folder, TESD remembers it and works in this
folder. If you decide to save your .para file in a certain directory and run a simulation, then the output .mea, .var and .frq files will be saved in this directory.
File
names
When you save parameters of a simulation, the .para file name
is constructed from the simulation
name you entered initially : simulation name.para
If you run a simulation from this .para file, the ouput file names
will receveive a .simulx
prefix where x is the number of the simulation run.
Advice
We advice you to create a directory in which you will put all your TESD files, and create a new folder for each simulation.