COLORALN
NAME
coloraln.pl − colorize an alignment with consensus structure
SYNOPSIS
coloraln.pl [−r] [−n] [−c columns] [−s structure.ps] file.aln
DESCRIPTION
colorrna.pl 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.
OPTIONS
−s file
read file to extract the consensus structure (default: "alirna.ps")
−c width
break alignments into blocks of at most width columns, (default: 120)
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−t |
suppress conversion of "T" to "U", i.e. do not convert DNA to RNA, (default: convert to "U") | ||
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−r |
add a "ruler" below the alignment showing sequence positions | ||
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−n |
write sequence position at the end of each sequence line |