Summary:
Given a nucleotide (or aminoacid) data file, a tree and a
nucleotide, aminoacid or codon model, SlidingWindowAnalysis.bf
performs a series of optmizations to detemine MLE of parameters
for several ranges of sites of user specified length.
Input:
A nucleotide (or aminoacid) data file in any recognizable
format. HYPHY uses the following table
to translate nucleotide ambiguities (or aminoacid
characters). The user specifies the range (window) of sites to include in each analysis and
the amount by which the window is offset after each analysis.
Models: Any of the standard
nucleotide, aminoacid or
codon models can be selected for the analysis.
Output: HYPHY will generate a comma separated
file containing parameter estimates and ln-likelihoods for each "window". A sample of on-screen
output follows:
---- RUNNING SLIDING DATA WINDOW ANALYSIS ----
**** Read file HAL 9000:Programming:DNAProject:data:brown.nuc ****
**** 895 sites (85 of them are distinct), and 5 species. ****
Enter the width (in bp) of the data window:100
Enter the amount of shift at each step (in bp):90
Working on segment 0 - 100
Working on segment 90 - 190
Working on segment 180 - 280
Working on segment 270 - 370
Working on segment 360 - 460
Working on segment 450 - 550
Working on segment 540 - 640
Working on segment 630 - 730
Working on segment 720 - 820
Working on segment 810 - 894
Result
Processing Tools: N/A.
|