Choose the 'Manage SNPs' radio button. Press the 'Proceed' button.

Read the information and press the 'Proceed' button.

Choose an input file. Multiple files may be selected. File has to be a a valid PanGEA-SNP file. See specifications here.

Choose viewpoint of analysis. Should the analysis be done for each SNP-site separately or should SNP-sites mapping to the same reference sequence be grouped and analysed. The reference sequence centered (gene centered) analysis allows to estimate the number of reference sequences covered by the SNPs or the average number of SNP sites per reference sequence etc.

Analyse your data interactively and flexibly. Observe the high SNP-bias for the active subset (15:2). Enter more restrictive qualtiy demand, type '3' into maximum number of low alignment quality tokens in SNP neighborhood. This features eliminates SNPs being close to a homopolymer when the 454 SNP-identification was used.

Observe the reduced SNP bias in the active subse (2:1) unfortunately the number of SNP-sites is also dramatically reduced. Press the back button.

Choose the gene centered analysis and press 'Proceed'

Analyse the SNPs flexibly and interactively from the perspecitive of the 'reference sequences' (gene IDs) . You can analyse how many ESTs map to a SNP-site or the number of SNP-sites mapping to a certain reference sequence etc.

Press the export button.

Press the Export entire subset button and save the active subset of your SNPs into a output file.