Programs used to analyze data from Freq Seq Data. See the main documentation pages at:
The source code is divided in to several folders.
- FreqSeqWPF - the WPF client on windows
- FreqSeq- The library file containing the methods used by the GUI and command line programs.
- freqout - The command line program.
New Version on 9/27/2015
- Warning message if unequal length alleles are input into the program.
- Compiled binary version released for Ubuntu 14.04
New Version on 12/4/2013
- Bug in Smith-waterman-Gotoh alignment (The +/- sign on the penalty for the gap creation and extension was switched, leading to incorrect alignments)
- Bug in barcode assigner – barcodes within hamming distance of 1 were not being assigned.
- Reads gzipped fastq files (ending with .gz)
- Changed command line executable name to freqout
- Trimmed long sequences to within only 10 bp longer than the expected read to improve alignment speed and accuracy
- Increased hashing k-mer length to 9 to reduce the number of alignment candidates identified
- Automatically skipping reads less than 75 bp (minimum length can be set in XML).
- Output column names changed