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There are several consensus modes:
- JalView (Default) — it the mode 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. A character in the consensus is calculated based on the characters in the corresponding column and the value of the threshold:
- If the percentage value of a character is greater than the threshold, the character is shown in upper case in the consensus.
- If there are two characters with high frequency in a column, the '+" sign is shown.
- If the percentage value of a character is high, but lower than the specified threshold, the character is shown in lower case in the consensus.
- ClustalW — emulates the ClustalW program and file format behavior.
- Levitsky — this algorithm is proposed by Victor Levitsky to calculate , this mode calculates the consensus of DNA alignments. At first, it collects a DNA alignment, taking into account frequencies of characters in the whole alignment, i.e. not only one column. The algorithm includes these steps:
- Collect global alignment frequencies for every
- character using the extended
- For every column
- select the rarest
- character in the whole alignment with the percentage in the column greater or
- equal to the threshold value.
- Simple extended — a character of the consensus is calculated based on the characters in the corresponding column. The extended DNA alphabet is used for the result consensus, the threshold value is also taken into account.
- Strict — the algorithm returns gap character (‘—’) if symbol frequency if a character percentage in a column is lower higher than the threshold specifiedspecified threshold, the character is shown in the consensus at this position. Otherwise, a gap character (‘—’) is shown.
Also the General tab shows the general information about an alignment and allows one to select set up a reference sequence. The following chapter describes how to export a consensus sequence:
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