Each base of a consensus sequence is calculated as a function of the corresponding column bases. The Chromatogram Editor allows switching between different consensus modes: Simple extended and Strict.
The Simple extended algorithm selects the best character from the extended DNA alphabet. Only bases with frequences which are greater than a threshold value are taken into account.
The Strict algorithm returns gap character ('-') if symbol frequency in a column is lower than threshold specified.
To switch the consensus mode go to the Consensus tab of the Options Panel:
There are several consensus modes:
- JalView (Default) — it is based on the JalView algorithm. Returns ‘+’ if there are 2 characters with high frequency. Returns symbol in lower case if the symbol content in a row is lower than the specified threshold.
- ClustalW — emulates the ClustalW program and file format behavior.
- Levitsky — this algorithm is proposed by Victor Levitsky to calculate consensus of DNA alignments. At first, it collects global alignment frequencies for every symbol using extended (15 symbols) DNA alphabet. Then, for every column it selects the rarest symbol in the whole alignment with percentage in the column greater or equals to the threshold value.
- Strict — the algorithm returns gap character (‘—’) if symbol frequency in a column is lower than the threshold specified.
Also the General tab shows the general information about an alignment and allows to select a reference sequence. The following chapter describes how to export a consensus sequence: