Software

There are various ways of viewing the aligned sequences in order to make it easy to locate SNPs and Locus specific differences.

• Jalview was highly recommended (www.ebi.ac.uk/~michele/jalview/).
• AgCanada has also developed some scripts to make viewing easier (contact D. Somers for details of access).
• There is also some viewing and snp mining software developed by David Edwards at Bristol (AutoSNP) that may become available in the future.
• Agrogene also has a proprietary viewer system -- however this software is not available for distribution, but it can be used on request to produce output files for contigs.
• Also check out BioEdit, http://www.mbio.ncsu.edu/BioEdit/bioedit.html. David Marshall of SCRI says, "We use this extensively together with GeneDoc for general sequence analysis. Bioedit has some drawbacks. It falls over after extensive use due to memory leakage but the benefits far outweigh the disadvantages."
• GGsnp_update.pl. A script to extract a valid FASTA file of the "Unigenes" (contig consensus sequences + singletons) from the WheatSNP data files. See GGsnp_update_Help.txt for more information.
• New! SNPF, Single Nucleotide Polymorphism Finder. A Java program to analyze a multiple sequence alignment contig file and display the SNPs. From Daniel Nwankwo, JIC.