# This file can be edited to allow you to choose the
# appropriate alphabet.
# 
# 1. Either uncomment the alphabet your wish to use 
#                     OR
#    type in a new alphabet.
#    (Any line beginning with a '#' is a comment)
#
# 2. Choose File --> Save
# 3. Choose File --> Close
#
# The file will then be used by consensus/wconsensus.
#
#The alphabet information can be placed on the command line using the
#-A option (shown in the consensus-v4b examples) or it can be placed in
#a file identified with the -a option.  By default, the alphabet
#information is sought from a file called "alphabet" (whose existence
#is assumed in the wconsensus-v3d examples).  The alphabet information
#indicates which letters are used in the sequences being aligned.  The
#alphabet information also indicates the a priori probabilities of the
#letters when the -d option is used.  In the absence of the -d option,
#the a priori probabilities are taken to be the frequencies of the
#letters in the sequences being aligned.
#
#====================== alphabet (DEFAULT) ==========================
# This file is called "alphabet" and contains the alphabet for the
# sequences being aligned.  The alphabet is not case sensitive unless
# the -CS option is used.  This alphabet file indicates that the
# letters 'a' and 't' are complementary and that each letter occurs
# with the same a priori probability of 0.25.
a:t
c:g
#========================== alphabet ==========================
# This alphabet file indicates that 'a' and 't' occur with an a priori
# probability of 0.3 and that 'c' and 'g' occur with an a priori
# probability of 0.2.
#a:t 0.6
#c:g 0.4
#========================== alphabet ==========================
# This alphabet file indicates that 'a' and 'g' occur with an a priori
# probability of 0.3 and that 't' and 'c' occur with an a priori
# probability of 0.2.
#a:t 6:4
#c:g 4:6
#========================== alphabet ==========================
# This alphabet file does not indicate which base pairs are
# complementary.  The a priori probabilities are 0.1, 0.2, 0.3, and 0.4
# for 'a', 't', 'c', and 'g', respectively.
#
#a 1
#t 2
#c 3
#g 4