fastaview.py 

Converts fasta format sequence alignments to an interleaved format
more suitable for viewing. Can also display differences from the 
consensus. Blocksize and line length can be specified.

Use the command
$ fastaview [alignment1] [alignment2] ... [alignmentn] | less 
to view the sequence one page at a time.

-w             { [60] } Line width
-blo           { [10] } Number of characters in each block; for
               example, set -blo=3 to view codon structure. -blo=0
               turns blocks off.
-nonum         Suppress numbering of positions
-dif           { [.] } display positions in each sequence identical
               to the consensus as a (.) by default or the specified
               character
-con           calculate consensus and display at the end of the
               alignment
-conseq        specify a sequence from the alignment by name to
               be used as the consensus. 
-plu           { [2] } pluarality for calculating consensus
-hea           Include header lines
-out           name of output file. Writes to screen by defult.
-h             Print documentation
-version       print version info and exit

$Id: fastaview.py,v 1.1 2004/10/10 02:53:10 nghoffma Exp $