AFLP analysis has emerged as a popular method for genetic mapping, species identification and phylogenetic analysis. The use of automated sequence machines to generate fluorescent AFLP (FAFLP) data makes this technique especially time and cost effective. The volume of data generated, however, requires substantial time for analysis. Manual peak scoring and existing software can introduce significant bias and errors. BinThere is a software tool that significantly reduces analysis time and eliminates many of these biases and scoring errors. It allocates fragment data into bins using one of two user-selected algorithms. In addition, BinThere provides access to the raw trace data and can use the raw data to calculate intensity readings at any point along the trace. BinThere was used to bin FAFLP data in an unbiased manner in order to examine the effects of varied reagent concentrations and gel compositions on the repeatability of FAFLP. Variation in a range of typical experimental conditions did not significantly impact reproducibility of the FAFLP method.
BinThere automatically bins GeneScan AFLP peak data. It reads data directly from ABI GeneScan 373 or 377 sample files. The user enters the range of fragment sizes and bin boundaries to analyze and the program can bin either with pre-set, uniformly distributed bin boundaries, or input-determined ("expert") bin boundaries. The output can be either tab-delimited text or NEXUS format. In addition, the user can chose additional information to be output along with fragment sizes. (See example of binning with just bp sizes. Example with bp sizes and peak height).
BinThere can also be used to output the intensity readings for any given set of uniformly distributed points in a trace reading. Additionally, a table of Peason's corellation coefficients based on the intensity readings can be automatically generated using BinThere.
The program is written in Java and uses the Java 1.1 API. I have provided a Macintosh exucutable which requires a Java interpretor to run. You can download Apple MRJ at this link if you don't already have it.
This program is distributed under the GNU General Public License.
Latest Update 4/24/00
Please send me any input you have. Both positive and negative comments are helpful.
Download Mac application (Aladdin InstallerMaker license has been applied for...)
Send mail to garnhart@cisunix.unh.edu