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Ambiguity Consensus Maker

Purpose: Make a consensus of IUPAC ambiguity codes for an alignment, or for blocks of sequences in an alignment. This tool works only for nucleotide alignments.

Usage: Browse or paste your alignment, choose options, and click "Run". You can specify the character presence percentage, which is the minimum representation required for a character to be considered in computing the consensus for that column. For example, a column containing 99 "A" and 1 "G" will be scored as "R" if the percentage is 0, but will be scored as "A" if the character presence is set at 1% or greater. In the latter case, the G would be ignored since it does not exceed 1% of the total. Note that all characters other than ACGTU are ignored. For details, see Ambiguity Consensus Maker Explanation.

Input
Paste your alignment
[Sample Input]
Or browse for your file
Squeeze gaps in input  Yes  No      Gap character
Output Options
Do consensus for each block  Yes  No
Minimum number of sequences for consensus
Show both consensus + alignment  Yes  No
Show number of sequences in consensus  Yes  No
Output format  Pretty  Output aligned  Like input
Consensus-making Options
Character presence percentage

last modified: Thu Jun 19 15:13 2014


Questions or comments? Contact us at seq-info@lanl.gov.

 
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