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NAME − colorize an alignment with consensus structure

SYNOPSIS [−r] [−n] [−c columns] [−s] file.aln

DESCRIPTION reads an alignment in CLUSTAL format, and a consensus secondary structure (which it extracts from a postscript secondary structure plot). It produces a postscript figure of the alignment, in which compensatory mutation supporting the consensus structure are marked by color. The color scheme is the same employed by RNAalifold and alidot: Red marks pairs with no sequence variation; ochre, green, turquoise, blue, and violet mark pairs with 2,3,4,5,6 different tpyes of pairs, respectively.


−s file

read file to extract the consensus structure (default: "")

−c width

break alignments into blocks of at most width columns, (default: 120)


suppress conversion of "T" to "U", i.e. do not convert DNA to RNA, (default: convert to "U")


add a "ruler" below the alignment showing sequence positions


write sequence position at the end of each sequence line