############################################################
# Example configuration file for mlocarna
##
# This file demonstrates the file format for configuring mlocarna from
# file.
#
# Use this file as argument to mlocarna's option --config to set
# (default) option values as specified below.
############################################################


# The file format is yaml-ish. Option value pairs are specified as
# option: value like in the following specification of the minimal
# probability
#
#-- Set slightly higher min-prob than mlocarna default
min-prob:	0.01


# Some more parameters can be set as follows, where white space and
# comments are ignored.

#-- better gap costs
indel:		-150 # this is much cheaper than the default
indel-opening:	-750 # in turn, raise the indel opening cost


# whitespace is allowed even preceeding the option name

#-- some sequence score contribution for structure matches
  tau: 50


# Besides option value pairs, also single options can be
# specified. Here are two examples:

#-- turn on probabilistic alignment with consistency-transformation
probabilistic
consistency-transformation

#options without values should *never* be used with values, since
# e.g. the following would turn *on* verbose mode, instead of turning
# it off
verbose: false # DON'T DO THIS AT HOME

## Finally, define some more useful parameters just for the fun of it.

#-- set moderate heuristics suited for global alignment
max-diff:	60
max-diff-am:	35

# use local folding
plfold-span:	100