School of Botany and Zoology
SOFTWARE DOWNLOAD PAGE
SiScan (Sister Scanning)
SiScan Version 2.0 (May
2001)
"Sister-scanning"
is a method for measuring variations in the relatedness of aligned nucleotide
sequences along their length. These variations result from recombination, from
differential selection or from random changes. The significance of detected
variations is tested in the program using Monte Carlo randomization procedures.
This enables misleading signals resulting from, for example, similarities of
composition, to be discounted. In this,Version 2.0, 'synonymous',
'non-synonymous' and all differences between sequences can be examined
separately. The SiScan program produces an output file in MS-Excel format, so
that the signals, and Z scores based on them, may be displayed graphically.
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RAPDistance (Analysis of RAPD
data.)
Version 1.04 is the latest
update of the original package. It has many associated programs and it is
capable of producing tree diagrams as postscript files. It also produces data
files in different formats so that other applications such as PHYLIP,WINAMOVA,
DIPLOMO, etc can be used. In response to many requests Version 2.00 has been
developed to enable much larger datasets to be examined. However it does not
have all the functions of the original version as programs for drawing trees
are limited to about 200 samples. These programs which come from other
programmers are memory limited; one, for example, uses a recursive routine
which requires large amounts of storage. The README files in th epackages give
more details of the differences. We have fully functional packages of Version
1.04 with other limits, which we will send when requested.
Version 1.04 Limits: 100
Samples, 20 Populations, 250 Bands,20 Primers
Version 2.00 Limits: 250
Samples, 50 Populations, 3000 Bands,50 Primers
Download
RAPDistance Version 1.04
Download
RAPDistance Version 2.00
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The GPRIME_2 Package
This package contains
programs to help with the design of PCR primers for a group of aligned related
nucleotide sequences; it is also useful for searching sequences for
taxonomically informative differences.
It is written in Fortran and operates under DOS in the Command Line via
a simple Batch file menu, and the outputs require a line editor and Excel. The aligned sequences are examined
using a sliding window technique to find regions of minimal variability. The programs calculate properties of
potential primer sites, namely their Tm, self- and cross-hybridization
potential, and there is also a program for searching a file of sequences with a
redundant sequence. The sequences must be provided in a single file in NBRF/PIR
or FASTA format. This version will handle up to 100
sequences, each of 25,000 nucleotides.