

name 
Name of the model.

tailp 
Fraction of the highest scores used to fit the distribution. For
Viterbi, MSV, and Hybrid scores, this defaults to 1.0 (a Gumbel
distribution is fitted to all the data). For Forward scores, this
defaults to 0.02 (an exponential tail is fitted to the highest 2%
scores).

mu/tau 
Location parameter for the maximum likelihood fit to the data.

lambda 
Slope parameter for the maximum likelihood fit to the data.

E@10 
The Evalue calculated for the 10th ranked high score (’E@10’) using the ML
mu/tau and lambda. By definition, this expected to be about 10, if
Evalue estimation were accurate.

mufix 
Location parameter, for a maximum likelihood fit with a known (fixed)
slope parameter lambda of log_2 (0.693).

E@10fix  
The Evalue calculated for the 10th ranked score using mufix and the
expected lambda = log_2 = 0.693.
 
mufix2 
Location parameter, for a maximum likelihood fit with an
edgeeffectcorrected lambda.

E@10fix2  
The Evalue calculated for the 10th ranked score using mufix2 and the
edgeeffectcorrected lambda.
 
pmu 
Location parameter as determined by H3’s estimation procedures.

plambda  
Slope parameter as determined by H3’s estimation procedures.
 
pE@10 
The Evalue calculated for the 10th ranked score using pmu, plambda.

Some of the optional output files are in xmgrace xy format. xmgrace is powerful and freely available graphplotting software.
h Help; print a brief reminder of command line usage and all available options.
a Collect expected Viterbi alignment length statistics from each simulated sequence. This only works with Viterbi scores (the default; see vit). Two additional fields are printed in the output table for each model: the mean length of Viterbi alignments, and the standard deviation.
v (Verbose). Print the scores too, one score per line.
L <n> Set the length of the randomly sampled (nonhomologous) sequences to <n>. The default is 100.
N <n> Set the number of randomly sampled sequences to <n>. The default is 1000.
mpi Run in MPI parallel mode, under mpirun. It is parallelized at the level of sending one profile at a time to an MPI worker process, so parallelization only helps if you have more than one profile in the <hmmfile>, and you want to have at least as many profiles as MPI worker processes. (Only available if optional MPI support was enabled at compiletime.)
o <f> Save the main output table to a file <f> rather than sending it to stdout.
afile <f> When collecting Viterbi alignment statistics (the a option), for each sampled sequence, output two fields per line to a file <f>: the length of the optimal alignment, and the Viterbi bit score. Requires that the a option is also used.
efile <f> Output a rank vs. Evalue plot in XMGRACE xy format to file <f>. The xaxis is the rank of this sequence, from highest score to lowest; the yaxis is the Evalue calculated for this sequence. Evalues are calculated using H3’s default procedures (i.e. the pmu, plambda parameters in the output table). You expect a rough match between rank and Evalue if Evalues are accurately estimated.
ffile <f> Output a "filter power" file to <f>: for each model, a line with three fields: model name, number of sequences passing the Pvalue threshold, and fraction of sequences passing the Pvalue threshold. See pthresh for setting the Pvalue threshold, which defaults to 0.02 (the default MSV filter threshold in H3). The Pvalues are as determined by H3’s default procedures (the pmu,plambda parameters in the output table). If all is well, you expect to see filter power equal to the predicted Pvalue setting of the threshold.
pfile <f> Output cumulative survival plots (P(S>x)) to file <f> in XMGRACE xy format. There are three plots: (1) the observed score distribution; (2) the maximum likelihood fitted distribution; (3) a maximum likelihood fit to the location parameter (mu/tau) while
assuming lambda=log_2.
xfile <f> Output the bit scores as a binary array of doubleprecision floats (8 bytes per score) to file <f>. Programs like Easel’s eslhistplot can read such binary files. This is useful when generating extremely large sample sizes.
H3 only uses multihit local alignment ( fs mode), and this is where we believe the statistical fits. Unihit local alignment scores (Smith/Waterman; sw mode) also obey our statistical conjectures. Glocal alignment statistics (either multihit or unihit) are still not adequately understood nor adequately fitted.
fs Collect multihit local alignment scores. This is the default. alignment as ’fragment search mode’.
sw Collect unihit local alignment scores. The H3 J state is disabled. alignment as ’Smith/Waterman search mode’.
ls Collect multihit glocal alignment scores. In glocal (global/local) alignment, the entire model must align, to a subsequence of the target. The H3 local entry/exit transition probabilities are disabled. ’ls’ comes from HMMER2’s historical terminology for multihit local alignment as ’local search mode’.
s Collect unihit glocal alignment scores. Both the H3 J state and local entry/exit transition probabilities are disabled. ’s’ comes from HMMER2’s historical terminology for unihit glocal alignment.
vit Collect Viterbi maximum likelihood alignment scores. This is the default.
fwd Collect Forward logodds likelihood scores, summed over alignment ensemble.
hyb Collect ’Hybrid’ scores, as described in papers by Yu and Hwa (for instance, Bioinformatics 18:864, 2002). These involve calculating a Forward matrix and taking the maximum cell value. The number itself is statistically somewhat unmotivated, but the distribution is expected be a wellbehaved extreme value distribution (Gumbel).
msv Collect MSV (multiple ungapped segment Viterbi) scores, using H3’s main acceleration heuristic.
fast For any of the above options, use H3’s optimized production implementation (using SIMD vectorization). The default is to use the implementations sacrifice a small amount of numerical precision. This can introduce confounding noise into statistical simulations and fits, so when one gets superconcerned about exact details, it’s better to be able to factor that source of noise out.
In some experiments, it was useful to fit Forward scores to a range of different tail masses, rather than just one. These options provide a mechanism for fitting an evenlyspaced range of different tail masses. For each different tail mass, a line is generated in the output.
tmin <x> Set the lower bound on the tail mass distribution. (The default is 0.02 for the default single tail mass.)
tmax <x> Set the upper bound on the tail mass distribution. (The default is 0.02 for the default single tail mass.)
tpoints <n> Set the number of tail masses to sample, starting from tmin and ending at tmax. (The default is 1, for the default 0.02 single tail mass.)
tlinear Sample a range of tail masses with uniform linear spacing. The default is to use uniform logarithmic spacing.
H3 uses three short random sequence simulations to estimating the location parameters for the expected score distributions for MSV scores, Viterbi scores, and Forward scores. These options allow these simulations to be modified.
EmL <n> Sets the sequence length in simulation that estimates the location parameter mu for MSV Evalues. Default is 200.
EmN <n> Sets the number of sequences in simulation that estimates the location parameter mu for MSV Evalues. Default is 200.
EvL <n> Sets the sequence length in simulation that estimates the location parameter mu for Viterbi Evalues. Default is 200.
EvN <n> Sets the number of sequences in simulation that estimates the location parameter mu for Viterbi Evalues. Default is 200.
EfL <n> Sets the sequence length in simulation that estimates the location parameter tau for Forward Evalues. Default is 100.
EfN <n> Sets the number of sequences in simulation that estimates the location parameter tau for Forward Evalues. Default is 200.
Eft <x> Sets the tail mass fraction to fit in the simulation that estimates the location parameter tau for Forward evalues. Default is 0.04.
stall For debugging the MPI master/worker version: pause after start, to enable the developer to attach debuggers to the running master and worker(s) processes. Send SIGCONT signal to release the pause. (Under gdb: (gdb) signal SIGCONT) (Only available if optional MPI support was enabled at compiletime.)
seed <n> Set the random number seed to <n>. The default is 0, which makes the random number generator use an arbitrary seed, so that different runs of hmmsim will almost certainly generate a different statistical sample. For debugging, it is useful to force reproducible results, by fixing a random number seed.
These options were used in a small variety of different exploratory experiments.
bgflat Set the background residue distribution to a uniform distribution, both for purposes of the null model used in calculating scores, and for generating the random sequences. The default is to use a standard amino acid background frequency distribution.
bgcomp Set the background residue distribution to the mean composition of the profile. This was used in exploring some of the effects of biased composition.
xnolengthmodel Turn the H3 target sequence length model off. Set the selftransitions for N,C,J and the null model to 350/351 instead; this emulates HMMER2. Not a good idea in general. This was used to demonstrate one of the main H2 vs. H3 differences.
nu <x> Set the nu parameter for the MSV algorithm  the expected number of ungapped local alignments per target sequence. The default is 2.0, corresponding to a E>J transition probability of 0.5. This was used to test whether varying nu has significant effect on result (it doesn’t seem to, within reason). This option only works if msv is selected (it only affects MSV), and it will not work with fast (because the optimized implementations are hardwired to assume nu=2.0).
pthresh <x> Set the filter Pvalue threshold to use in generating filter power files with ffile. The default is 0.02 (which would be appropriate for testing MSV scores, since this is the default MSV filter threshold in H3’s acceleration pipeline.) Other appropriate choices (matching defaults in the acceleration pipeline) would be 0.001 for Viterbi, and 1e5 for Forward.
See hmmer(1) for a master man page with a list of all the individual man pages for programs in the HMMER package.
For complete documentation, see the user guide that came with your HMMER distribution (Userguide.pdf); or see the HMMER web page (@HMMER_URL@).
@HMMER_COPYRIGHT@ @HMMER_LICENSE@For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or see the HMMER web page (@HMMER_URL@).
Eddy/Rivas Laboratory Janelia Farm Research Campus 19700 Helix Drive Ashburn VA 20147 USA http://eddylab.org
HMMER @HMMER_VERSION@  HMMSIM (1)  @HMMER_DATE@ 
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