HMM Format

Example

Below is a two-state model generated using the default values. Comments (ignored by the program) are shown in red and the actual parameter values in black. Comments in blue are additional explanation and not found in a standard .hmm file.

# Number of states   (obvious, isn't it? This is a two-state model!)
2
# Alphabet   (specifies DNA, RNA or protein -- or any other alphabet)
ACGT
# equilibrium distributions   (character frequencies for each state [1 and 2 here])

0.25 0.25 0.25 0.25 
0.25 0.25 0.25 0.25 
# Scaled Q matrices   (Q is instantaneous rate matrix, separately for each state)
# Model 1 ; scale = 0.855871   ('scale' can be seen as divider for branch length;
-1.1684 0.389467 0.389467 0.389467    as it is less than 1, branches are longer
0.389467 -1.1684 0.389467 0.389467    and sites are expected to evolve faster)
0.389467 0.389467 -1.1684 0.389467 
0.389467 0.389467 0.389467 -1.1684 
# Model 2 ; scale = 1.33333   ('scale' is greater than 1, so branches are shorter

-0.75 0.25 0.25 0.25            and sites are expected to evolve more slowly)
0.25 -0.75 0.25 0.25 
0.25 0.25 -0.75 0.25 
0.25 0.25 0.25 -0.75 
# Structure background probabilities   (starting probability -- equal so no info)
0.5 0.5
# Structure transition probabilities   (probability to move from one structure to
0.9667 0.0333                         another or to stay in a structure [diagonal])

0.0500 0.9500
# Indel rates   (indel rates in the two structures; 2nd seems to have fewer indels)
0.0500 0.0250
# Indel extension probabilities   (indel lengths; 2nd seems to have shorter indels)
0.8000 0.5000
# Match extension probabilities   (for completeness; better kept 0?)
0 0
# Codon position   (two structures are non-coding; otherwise 1, 2 or 3)
0 0

# Draw pattern   (for visualisation in kprank)
2 2
# Draw color   (for visualisation in kprank)
2 1
# Draw offset   (for visualisation in kprank)
1 1
# State name   (for visualisation in kprank)
process1 process2