svr_ali_to_html

Introduction

    svr_ali_to_html [options] < alignment.in.fasta.format > alignment.as.html

Convert a FASTA alignment to HTML

This script takes a FASTA version of an alignment and produces the HTML needed to support visualization of the alignment.

Command-Line Options

-c=conservation|conservation2|residue|none

If conservation is specified, coloring is used to reveal levels of conservation (within a column). If conservation2 is specified, an alternative color scheme is used to reveal levels of conservation (within a column). If residue is specified, coloring is used to reveal classes of residues. If none simply turns off coloring

The default value is conservation.

-d

If this option is specified, pop-up sequence definitions (comments) will be omitted

-j

If this option is specified, pop-up menus will be omitted (only valid with -t)

-l

If this option is specified, the legend will be omitted

-n

Treat residues as nucleotides (if neither -n nor -p is set, the program looks at the sequence and guesses)

-p

Treat residues as amino acids (if neither -n nor -p is set, the program looks at the sequence and guesses)

-s=seqfile

Add unaligned residues to the ends of the alignment

-t

Write html table (default is to write a self-contained page)

Output Format

The generated HTML document is written to STDOUT.