# This is a comment
# The first thing in the file must be the Multi-FASTA file

sample.fasta

# The rest of the parameters can be in any order.
# Compound parameters must be on one line.


# Base sequence MUST appear before sequence pairs

# Optional base sequence (default is the first sequence in file).
sample1

# Optional pairs
sample1 sample2
sample1 sample3
sample2 sample3


# MLAGAN parameters
# preceded by "-"

# Phylogenetic tree specification (required). 
#-tree "(...)"

-tree "((sample1 sample2) sample3)"

# Lazy evaluation... 
#-lazy

# Nested Iterative Refinement
#-nested

# Turning on post-alignment Iterative Refinement
#-postir

# VISTA parameters (defaults)
# preceded by "--"

# ALIGN REGION MIN (75), REGION MAX (100), MIN (50)
#--regmin 75
#--regmax 100
#--min 50

# BASES (10000)
#--bases 10000

# TICK DISTANCE (2000)
#--tickdist 1000

# RESOLUTION (25)
#--resolution 25

# WINDOW (70)
#--window 70

# NUM WINDOWS (4)
#--numwindows 4