Data analysis tools and simulation programs for telomeres dynamics
## The code enclosed was developed by M. Hidalgo-Soria
## Contact mariohidalgosoria@gmail.com
### The following tools were used in experimental telomere tracks
with 50 and 100 steps of time.


The tools and codes are distributed in directories as follows:

1) For performing data analysis of telomere tracks.
-> The folder 'Data_Analysis' contains sub-directories:
--> 'Drift_Rot_Corr' with C programs for correcting drift and rotation
of experimental trajectories, read inner README file.
--> 'Rel_Ang' with C programs for computing the relative angle in
experimental tracks. 
--> '2State_Decomp' contains C programs for decomposing tracks into intervals
according to its level of persistence and to its relative jumps size. 
--> 'MSD' contains C programs for computing time average MSD, ensemble time
average MSD and ensemble MSD.  
--> 'ACFDXDY' contains C programs for computing the auto correlation function
of displacements on X and Y axes, for different intervals of time.
--> 'TAV_RA' contains C programs for computing the time average relative angle
per trajectories.
--> 'Pair_Wise_Corr' contains C programs for computing the autocorrelation 
function of the pair-wise directional displacements of telomeres in the same cell.

2) For performing simulations of a switching models with caging and pure diffusive
phases for WT cells and varying persistent and pure diffusive phases for KO cells.
-> The folder 'Simulations' contains programs for simulating telomeres
dynamics in wild type cells and telomeres in Lamin-A depleted cells. 


3) For plotting the results of experimental trajectories and simulated ones.
-> The folder 'Plots' contains files with generic octave and gnuplot routines
for:
--> plotting trajectories 'Fig1.txt'
--> PDF of displacements 'Fig2.txt'
--> PDF of relative angle 'Fig3.txt'
--> mean relative angle 'Fig4.txt'
--> autocorrelation function of the pair-wise directional 
displacements 'Fig5.txt'
--> comparison between experiments and numerical simulations 'Fig6.txt'
--> two state representation of trajectories 'Fig7.txt'
--> MSD analysis of experimental tracks 'FigS2.txt'
--> decay length of the PDF of displacements 'FigS3.txt'
--> autocorrelation function of displacements 'FigS4.txt'
--> PDF of the time average relative angle 'FigS5.txt'
--> autocorrelation function of the pair-wise directional 
displacements for a Pearson RW 'FigS6.txt'
--> schematic representation of local convex hull 'FigS7.txt'
--> PDF of waiting times 'FigS8.txt'
--> simulated trajectories with caging and free diffusion 'FigS9.txt'
--> data analysis of simulated trajectories with caging and free
diffusion 'FigS10.txt'
--> simulated trajectories with free diffusion  and varying persistence
'FigS11.txt'
--> data analysis of simulated trajectories with free diffusion and varying
persistence 'FigS12.txt'