letterconf command

Calculate letter confidences.

Examples

muscle -letterconf ensemble.efa -ref aln.afa -output lc.afa
muscle -letterconf ensemble.efa -ref aln.afa -output lc.afa \
-html lc.html -jalview jalview.features

Description

The letterconf command calculates letter confidence values. Output is in FASTA format where each letter is replaced by a letter confidence value 0..9 .

See also the addconfseq command which generates column confidence values.

The -html option specifies an HTML output file where the alignment is colored by confidence.

The -jalview option specifies a features file for Jalview . See Jalview features for more information.

Example Jalview and HTML display