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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

120,000 new RNA virus species discovered by mining the SRA (paper).

Syncmers are better than minimizers (paper).

Video talks on 16S data analysis posted.

URMAP ultra-fast read mapper (paper).

~20% of taxonomy annotations in SILVA and Greengenes are wrong (paper).

Taxonomy prediction is <50% accurate for 16S V4 sequences (paper).

97% OTU threshold is wrong for species, should be 99% for full-length 16S, 100% V4 (paper).