New module for shared korflab perl scripts and modules
Script to make a directory with symbolic links to perl scripts and/or modules which occur in another specified directory
typo fix
Small bunch of changes:

1) Colors of nucleotides in motif picture file now agree with colors produced by NestedMICA motif viewer program, except...

2) Yellow is changed to orange for better visibility against white background

3) Small changes to font declarations in SVG file to remove unnecessary single quotes which were causing problems for ImageMagick
to convert SVG to PNG files

4) For logo output, nucleotides are now arranged in height order (biggest/heighest nucleotide on top). This is the same as
NestedMICA

5) pictogram output still is in A,C,G,T order irrespective of size

Keith
1) Motif.pm is now slightly more permissive when importing XMS files, the motifset tag has to be present but now
it doesn't need any other information after the tag

2) references to biotiffin.org removed from output xms files as this Web site is not live at the moment
Changed script to include Korf lab banner logo
a simple script to just check whether a FASTA file contains duplicate sequence entries
slight tweak to now include number of duplicate entries in output
kl distance script, handles up to a word size of 10 nt
New script to shuffle a FASTA sequence file
You can specify the size of oligomer that you wish to shuffle by, e.g. 1 = shuffling by nucleotides, 5 = shuffling by pentamers
You can also choose how many shuffled files to create.

E.g. shuffle_seq.pl input.fa 2 100

This would create 100 output files (named after the input file with .r1, .r2 etc. suffixes) which were each generated by
shuffling dinucleotide frequencies of sequences in the input file.

Keith
Moved feedback section to bottom of page
Added a check that counts how many possible words only exist as pseudocounts. I.e if you calculate the KL distance with
a large word size (7,8... etc) then many possible words might not exist in your input files (especially if the files
are relatively small).

In this case, the K-L distance may be calculated based on lots of 1 vs 1 calculations for individual word counts.
The script now calculates what percentage of all possible words do not exist in each input file and warns
if this is greater than 10%. This is an arbitrary threshold value, but should hopefully point to using a smaller
word size for a more meaningful KL distance
reduced threshold for sequences that have only pseudocounted word values. Will now warn if more than 5 percent of all possible words only exist as pseudocounts. Was previously set to 10 percent
New companion script to kl_distance.pl Will take the KL distance between two files (A & B)
and then try to see how significant that is. First it splits file A into two new files, each
containing half of the sequences (randomly chosen) from the parent fie. For up to N times,
it calculates the KL distance between these two split files and counts how many times the
original distance was exceeded.

If you set N (the 4th parameter on the command line) to be 100, then you can simply say
that if the original distance was exceeded more than 5 times out of 100 then the original
KL distance was not significant.

It then repeats this shuffling for the 2nd file (which can give different results if there
is more or less heterogeneity in this file). Finally it randomizes the DNA of each
file (preserving mononucleotide frequencies) and asks how many times (out of N randomizations)
the original KL distance is exceeded.

Can be slow with large files and/or large word sizes.
A new script in the family of KL distance scripts. This calculates a KL distance between two
sets of sequences and then randomizes each set (N) times and calculates KL distances again.

From the distribution of KL distances in the randomized data, it can calculate a Z
statistic to see how far away the observed KL distance (from the real data) is from the mean
KL distance in the randomized data
added many comments
add new option for indexing
Redesigned atcg.pl which now makes use of a new package (Keith.pm)

Includes improved and new command-line options as well as better
error checking (e.g. when sequence does not contain any nucleotides).
New perl module which will (hopefully) contain many of the subroutines
that I frequently use. Currently has one function to calculate
mononucleotides in any specified string.
New script to calculate dinucleotide frequencies which borrows from a new
function in Keith.pm
Updated perldoc