static void
utest_Compare(void)
{
  ESL_RANDOMNESS *r    = esl_randomness_CreateFast(42);
  ESL_ALPHABET   *abc  = esl_alphabet_Create(eslAMINO);
  P7_HMM         *hmm  = NULL;
  P7_BG          *bg   = NULL;
  P7_PROFILE     *gm   = NULL;
  P7_PROFILE     *gm2  = NULL;
  int             M    = 200;
  int             L    = 400;

  p7_modelsample(r, M, abc, &hmm); /* master and worker's sampled profiles are identical */
  bg  = p7_bg_Create(abc);

  gm  = p7_profile_Create(hmm->M, abc);
  gm2 = p7_profile_Create(hmm->M, abc);

  p7_profile_Config(gm,  hmm, bg);
  p7_profile_Config(gm2, hmm, bg);

  p7_profile_SetLength(gm,  L);
  p7_profile_SetLength(gm2, L);

  if (p7_profile_Compare(gm, gm2, 0.001) != eslOK) p7_Die("identical profile comparison failed");
  
  p7_profile_Destroy(gm);
  p7_profile_Destroy(gm2);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  esl_alphabet_Destroy(abc);
  esl_randomness_Destroy(r);
  return;
}

/* The MSV score can be validated against Viterbi (provided we trust
 * Viterbi), by creating a multihit local profile in which:
 *   1. All t_MM scores = 0
 *   2. All other core transitions = -inf
 *   3. All t_BMk entries uniformly log 2/(M(M+1))
 */
static void
utest_msv(ESL_GETOPTS *go, ESL_RANDOMNESS *r, ESL_ALPHABET *abc, P7_BG *bg, P7_PROFILE *gm, int nseq, int L)
{
  P7_PROFILE *g2 = NULL;
  ESL_DSQ   *dsq = NULL;
  P7_GMX    *gx  = NULL;
  float     sc1, sc2;
  int       k, idx;

  if ((dsq    = malloc(sizeof(ESL_DSQ) *(L+2))) == NULL)  esl_fatal("malloc failed");
  if ((gx     = p7_gmx_Create(gm->M, L))        == NULL)  esl_fatal("matrix creation failed");
  if ((g2     = p7_profile_Clone(gm))           == NULL)  esl_fatal("profile clone failed");

  /* Make g2's scores appropriate for simulating the MSV algorithm in Viterbi */
  esl_vec_FSet(g2->tsc, p7P_NTRANS * g2->M, -eslINFINITY);
  for (k = 1; k <  g2->M; k++) p7P_TSC(g2, k, p7P_MM) = 0.0f;
  for (k = 0; k <  g2->M; k++) p7P_TSC(g2, k, p7P_BM) = log(2.0f / ((float) g2->M * (float) (g2->M+1)));

  for (idx = 0; idx < nseq; idx++)
    {
      if (esl_rsq_xfIID(r, bg->f, abc->K, L, dsq) != eslOK) esl_fatal("seq generation failed");

      if (p7_GMSV    (dsq, L, gm, gx, 2.0, &sc1)       != eslOK) esl_fatal("MSV failed");
      if (p7_GViterbi(dsq, L, g2, gx,      &sc2)       != eslOK) esl_fatal("viterbi failed");
      if (fabs(sc1-sc2) > 0.0001) esl_fatal("MSV score not equal to Viterbi score");
    }

  p7_gmx_Destroy(gx);
  p7_profile_Destroy(g2);
  free(dsq);
  return;
}

/* ViterbiScore() unit test
 * 
 * We can compare these scores to GViterbi() almost exactly; the only
 * differences should be negligible roundoff errors. Must convert
 * the optimized profile to lspace, though, rather than pspace.
 */
static void
utest_viterbi_score(ESL_RANDOMNESS *r, ESL_ALPHABET *abc, P7_BG *bg, int M, int L, int N)
{
  P7_HMM      *hmm = NULL;
  P7_PROFILE  *gm  = NULL;
  P7_OPROFILE *om  = NULL;
  ESL_DSQ     *dsq = malloc(sizeof(ESL_DSQ) * (L+2));
  P7_OMX      *ox  = p7_omx_Create(M, 0, 0);
  P7_GMX      *gx  = p7_gmx_Create(M, L);
  float sc1, sc2;

  p7_oprofile_Sample(r, abc, bg, M, L, &hmm, &gm, &om);
  p7_oprofile_Logify(om);
  while (N--)
    {
      esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);

      p7_ViterbiScore(dsq, L, om, ox, &sc1);
      p7_GViterbi    (dsq, L, gm, gx, &sc2);

      if (fabs(sc1-sc2) > 0.001) esl_fatal("viterbi score unit test failed: scores differ");
    }

  free(dsq);
  p7_hmm_Destroy(hmm);
  p7_omx_Destroy(ox);
  p7_gmx_Destroy(gx);
  p7_profile_Destroy(gm);
  p7_oprofile_Destroy(om);
}

int 
main(int argc, char **argv)
{
  char           *msg  = "p7_gmx unit test driver failed";
  ESL_GETOPTS    *go   = p7_CreateDefaultApp(options, 0, argc, argv, banner, usage);
  ESL_RANDOMNESS *r    = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  ESL_ALPHABET   *abc  = esl_alphabet_Create(eslAMINO);
  P7_BG          *bg   = p7_bg_Create(abc);
  P7_HMM         *hmm  = NULL;
  P7_PROFILE     *gm   = NULL;
  int             M    = esl_opt_GetInteger(go, "-M");
  int             L    = esl_opt_GetInteger(go, "-L");
  float           tol  = esl_opt_GetReal   (go, "-t");

  p7_FLogsumInit();

  if (p7_hmm_Sample(r, M, abc, &hmm)                != eslOK) esl_fatal(msg);
  if ((gm = p7_profile_Create(hmm->M, abc))         == NULL)  esl_fatal(msg);
  if (p7_bg_SetLength(bg, L)                        != eslOK) esl_fatal(msg);
  if (p7_ProfileConfig(hmm, bg, gm, L, p7_UNILOCAL) != eslOK) esl_fatal(msg);

  utest_GrowTo();
  utest_Compare(r, gm, bg, L, tol);

  esl_getopts_Destroy(go);
  esl_randomness_Destroy(r);
  esl_alphabet_Destroy(abc);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  p7_profile_Destroy(gm);
  return eslOK;
}

/* Function:  p7_oprofile_Sample()
 * Synopsis:  Sample a random profile.
 * Incept:    MSF Tue Nov 3, 2009 [Janelia]
 *
 * Purpose:   Sample a random profile of <M> nodes for alphabet <abc>,
 *            using <r> as the source of random numbers. Parameterize
 *            it for generation of target sequences of mean length
 *            <L>. Calculate its log-odds scores using background
 *            model <bg>.
 *            
 * Args:      r       - random number generator
 *            abc     - emission alphabet 
 *            bg      - background frequency model
 *            M       - size of sampled profile, in nodes
 *            L       - configured target seq mean length
 *            opt_hmm - optRETURN: sampled HMM
 *            opt_gm  - optRETURN: sampled normal profile
 *            opt_om  - RETURN: optimized profile
 *
 * Returns:   <eslOK> on success.
 *
 * Throws:    (no abnormal error conditions)
 */
int
p7_oprofile_Sample(ESL_RANDOMNESS *r, const ESL_ALPHABET *abc, const P7_BG *bg, int M, int L,
		   P7_HMM **opt_hmm, P7_PROFILE **opt_gm, P7_OPROFILE **ret_om)
{
  P7_HMM         *hmm  = NULL;
  P7_PROFILE     *gm   = NULL;
  P7_OPROFILE    *om   = NULL;
  int             status;

  if ((gm = p7_profile_Create (M, abc)) == NULL)  { status = eslEMEM; goto ERROR; }
  if ((om = p7_oprofile_Create(M, abc)) == NULL)  { status = eslEMEM; goto ERROR; }

  if ((status = p7_hmm_Sample(r, M, abc, &hmm))             != eslOK) goto ERROR;
  if ((status = p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL)) != eslOK) goto ERROR;
  if ((status = p7_oprofile_Convert(gm, om))                != eslOK) goto ERROR;
  if ((status = p7_oprofile_ReconfigLength(om, L))          != eslOK) goto ERROR;

  if (opt_hmm != NULL) *opt_hmm = hmm; else p7_hmm_Destroy(hmm);
  if (opt_gm  != NULL) *opt_gm  = gm;  else p7_profile_Destroy(gm);
  *ret_om = om;
  return eslOK;

 ERROR:
  if (opt_hmm != NULL) *opt_hmm = NULL;
  if (opt_gm  != NULL) *opt_gm  = NULL;
  *ret_om = NULL;
  return status;
}

int
main(int argc, char **argv)
{
    ESL_GETOPTS    *go      = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
    char           *hmmfile = esl_opt_GetArg(go, 1);
    ESL_STOPWATCH  *w       = esl_stopwatch_Create();
    ESL_RANDOMNESS *r       = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
    ESL_ALPHABET   *abc     = NULL;
    P7_HMMFILE     *hfp     = NULL;
    P7_HMM         *hmm     = NULL;
    P7_BG          *bg      = NULL;
    P7_PROFILE     *gm      = NULL;
    P7_GMX         *gx1     = NULL;
    P7_GMX         *gx2     = NULL;
    int             L       = esl_opt_GetInteger(go, "-L");
    int             N       = esl_opt_GetInteger(go, "-N");
    ESL_DSQ        *dsq     = malloc(sizeof(ESL_DSQ) * (L+2));
    float           null2[p7_MAXCODE];
    int             i;
    float           fsc, bsc;
    double          Mcs;

    if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
    if (p7_hmmfile_Read(hfp, &abc, &hmm)            != eslOK) p7_Fail("Failed to read HMM");

    bg = p7_bg_Create(abc);
    p7_bg_SetLength(bg, L);
    gm = p7_profile_Create(hmm->M, abc);
    p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL);
    gx1 = p7_gmx_Create(gm->M, L);
    gx2 = p7_gmx_Create(gm->M, L);

    esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
    p7_GForward (dsq, L, gm, gx1, &fsc);
    p7_GBackward(dsq, L, gm, gx2, &bsc);
    p7_GDecoding(gm, gx1, gx2, gx2);

    esl_stopwatch_Start(w);
    for (i = 0; i < N; i++)
        p7_GNull2_ByExpectation(gm, gx2, null2);
    esl_stopwatch_Stop(w);

    Mcs  = (double) N * (double) L * (double) gm->M * 1e-6 / w->user;
    esl_stopwatch_Display(stdout, w, "# CPU time: ");
    printf("# M    = %d\n", gm->M);
    printf("# %.1f Mc/s\n", Mcs);

    free(dsq);
    p7_gmx_Destroy(gx1);
    p7_gmx_Destroy(gx2);
    p7_profile_Destroy(gm);
    p7_bg_Destroy(bg);
    p7_hmm_Destroy(hmm);
    p7_hmmfile_Close(hfp);
    esl_alphabet_Destroy(abc);
    esl_stopwatch_Destroy(w);
    esl_randomness_Destroy(r);
    esl_getopts_Destroy(go);
    return 0;
}

int
main(int argc, char **argv)
{
  ESL_GETOPTS    *go    = esl_getopts_CreateDefaultApp(options, 0, argc, argv, banner, usage);
  ESL_RANDOMNESS *r    = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  ESL_ALPHABET   *abc  = NULL;
  P7_HMM         *hmm  = NULL;
  P7_PROFILE     *gm   = NULL;
  P7_BG          *bg   = NULL;
  int             M    = 100;
  int             L    = 200;
  int             nseq = 20;
  char            errbuf[eslERRBUFSIZE];

  if ((abc = esl_alphabet_Create(eslAMINO))         == NULL)  esl_fatal("failed to create alphabet");
  if (p7_hmm_Sample(r, M, abc, &hmm)                != eslOK) esl_fatal("failed to sample an HMM");
  if ((bg = p7_bg_Create(abc))                      == NULL)  esl_fatal("failed to create null model");
  if ((gm = p7_profile_Create(hmm->M, abc))         == NULL)  esl_fatal("failed to create profile");
  if (p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL)    != eslOK) esl_fatal("failed to config profile");
  if (p7_hmm_Validate    (hmm, errbuf, 0.0001)      != eslOK) esl_fatal("whoops, HMM is bad!: %s", errbuf);
  if (p7_profile_Validate(gm,  errbuf, 0.0001)      != eslOK) esl_fatal("whoops, profile is bad!: %s", errbuf);

  utest_basic  (go);
  utest_viterbi(go, r, abc, bg, gm, nseq, L);

  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  esl_alphabet_Destroy(abc);
  esl_randomness_Destroy(r);
  esl_getopts_Destroy(go);
  return 0;
}

/* The "basic" utest is a minimal driver for making a small DNA profile and a small DNA sequence,
 * then running Viterbi and Forward. It's useful for dumping DP matrices and profiles for debugging.
 */
static void
utest_basic(ESL_GETOPTS *go)
{
  char           *query= "# STOCKHOLM 1.0\n\nseq1 GAATTC\nseq2 GAATTC\n//\n";
  int             fmt  = eslMSAFILE_STOCKHOLM;
  char           *targ = "GAATTC";
  ESL_ALPHABET   *abc  = NULL;
  ESL_MSA        *msa  = NULL;
  P7_HMM         *hmm  = NULL;
  P7_PROFILE     *gm   = NULL;
  P7_BG          *bg   = NULL;
  P7_PRIOR       *pri  = NULL;	
  ESL_DSQ        *dsq  = NULL;
  P7_GMX         *gx   = NULL;
  P7_TRACE        *tr  = NULL;
  int             L    = strlen(targ);
  float           vsc, vsc2, fsc;

  if ((abc = esl_alphabet_Create(eslDNA))          == NULL)  esl_fatal("failed to create alphabet");
  if ((pri = p7_prior_CreateNucleic())             == NULL)  esl_fatal("failed to create prior");
  if ((msa = esl_msa_CreateFromString(query, fmt)) == NULL)  esl_fatal("failed to create MSA");
  if (esl_msa_Digitize(abc, msa, NULL)             != eslOK) esl_fatal("failed to digitize MSA");
  if (p7_Fastmodelmaker(msa, 0.5, NULL, &hmm, NULL) != eslOK) esl_fatal("failed to create GAATTC model");
  if (p7_ParameterEstimation(hmm, pri)             != eslOK) esl_fatal("failed to parameterize GAATTC model");
  if (p7_hmm_SetConsensus(hmm, NULL)               != eslOK) esl_fatal("failed to make consensus");
  if ((bg = p7_bg_Create(abc))                     == NULL)  esl_fatal("failed to create DNA null model");
  if ((gm = p7_profile_Create(hmm->M, abc))        == NULL)  esl_fatal("failed to create GAATTC profile");
  if (p7_ProfileConfig(hmm, bg, gm, L, p7_UNILOCAL)!= eslOK) esl_fatal("failed to config profile");
  if (p7_profile_Validate(gm, NULL, 0.0001)        != eslOK) esl_fatal("whoops, profile is bad!");
  if (esl_abc_CreateDsq(abc, targ, &dsq)           != eslOK) esl_fatal("failed to create GAATTC digital sequence");
  if ((gx = p7_gmx_Create(gm->M, L))               == NULL)  esl_fatal("failed to create DP matrix");
  if ((tr = p7_trace_Create())                     == NULL)  esl_fatal("trace creation failed");

  p7_GViterbi   (dsq, L, gm, gx, &vsc);
  if (esl_opt_GetBoolean(go, "-v")) printf("Viterbi score: %.4f\n", vsc);
  if (esl_opt_GetBoolean(go, "-v")) p7_gmx_Dump(stdout, gx, p7_DEFAULT);

  p7_GTrace     (dsq, L, gm, gx, tr);
  p7_trace_Score(tr, dsq, gm, &vsc2);
  if (esl_opt_GetBoolean(go, "-v")) p7_trace_Dump(stdout, tr, gm, dsq);
  
  if (esl_FCompare(vsc, vsc2, 1e-5) != eslOK)  esl_fatal("trace score and Viterbi score don't agree.");

  p7_GForward   (dsq, L, gm, gx, &fsc);
  if (esl_opt_GetBoolean(go, "-v")) printf("Forward score: %.4f\n", fsc);
  if (esl_opt_GetBoolean(go, "-v")) p7_gmx_Dump(stdout, gx, p7_DEFAULT);

  p7_trace_Destroy(tr);
  p7_gmx_Destroy(gx);
  free(dsq);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  esl_msa_Destroy(msa);
  p7_prior_Destroy(pri);
  esl_alphabet_Destroy(abc);
  return;
}

int 
main(int argc, char **argv)
{
  ESL_GETOPTS    *go      = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
  ESL_RANDOMNESS *rng     = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
  char           *hmmfile = esl_opt_GetArg(go, 1);
  int             L       = esl_opt_GetInteger(go, "-L");
  int             N       = esl_opt_GetInteger(go, "-N");
  ESL_ALPHABET   *abc     = NULL;
  P7_HMMFILE     *hfp     = NULL;
  P7_HMM         *hmm     = NULL;
  P7_BG          *bg      = NULL;
  P7_PROFILE     *gm      = NULL;
  P7_TRACE       *tr      = p7_trace_Create();
  ESL_SQ         *sq      = NULL;
  char            errbuf[eslERRBUFSIZE];
  int             i;
  int             status;

  status = p7_hmmfile_OpenE(hmmfile, NULL, &hfp, errbuf);
  if      (status == eslENOTFOUND) p7_Fail("File existence/permissions problem in trying to open HMM file %s.\n%s\n", hmmfile, errbuf);
  else if (status == eslEFORMAT)   p7_Fail("File format problem in trying to open HMM file %s.\n%s\n",                hmmfile, errbuf);
  else if (status != eslOK)        p7_Fail("Unexpected error %d in opening HMM file %s.\n%s\n",                       status, hmmfile, errbuf);  

  status = p7_hmmfile_Read(hfp, &abc, &hmm);
  if      (status == eslEFORMAT)   p7_Fail("Bad file format in HMM file %s:\n%s\n",          hfp->fname, hfp->errbuf);
  else if (status == eslEINCOMPAT) p7_Fail("HMM in %s is not in the expected %s alphabet\n", hfp->fname, esl_abc_DecodeType(abc->type));
  else if (status == eslEOF)       p7_Fail("Empty HMM file %s? No HMM data found.\n",        hfp->fname);
  else if (status != eslOK)        p7_Fail("Unexpected error in reading HMMs from %s\n",     hfp->fname);

  p7_hmmfile_Close(hfp);

  bg = p7_bg_Create(abc);                p7_bg_SetLength(bg, L);
  gm = p7_profile_Create(hmm->M, abc);   p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL);
  sq = esl_sq_CreateDigital(abc);

  for (i = 0; i < N; i++)
    {
      p7_ProfileEmit(rng, hmm, gm, bg, sq, tr);
      esl_sq_FormatName(sq, "%s-sample%d", hmm->name, i);
      esl_sqio_Write(stdout, sq, eslSQFILE_FASTA, FALSE);

      if (p7_trace_Validate(tr, abc, sq->dsq, errbuf) != eslOK) esl_fatal(errbuf);

      esl_sq_Reuse(sq);
      p7_trace_Reuse(tr);
    }      

  esl_sq_Destroy(sq);
  p7_trace_Destroy(tr);
  p7_profile_Destroy(gm);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  esl_alphabet_Destroy(abc);
  esl_randomness_Destroy(rng);
  esl_getopts_Destroy(go);
  return 0;
}

/* Function:  p7_Builder()
 * Synopsis:  Build a new HMM from an MSA.
 *
 * Purpose:   Take the multiple sequence alignment <msa> and a build configuration <bld>,
 *            and build a new HMM. 
 * 
 *            Effective sequence number determination and calibration steps require
 *            additionally providing a null model <bg>.
 *
 * Args:      bld         - build configuration
 *            msa         - multiple sequence alignment
 *            bg          - null model
 *            opt_hmm     - optRETURN: new HMM
 *            opt_trarr   - optRETURN: array of faux tracebacks, <0..nseq-1>
 *            opt_gm      - optRETURN: profile corresponding to <hmm>
 *            opt_om      - optRETURN: optimized profile corresponding to <gm>
 *            opt_postmsa - optRETURN: RF-annotated, possibly modified MSA 
 *
 * Returns:   <eslOK> on success. The new HMM is optionally returned in
 *            <*opt_hmm>, along with optional returns of an array of faux tracebacks
 *            for each sequence in <*opt_trarr>, the annotated MSA used to construct
 *            the model in <*opt_postmsa>, a configured search profile in 
 *            <*opt_gm>, and an optimized search profile in <*opt_om>. These are
 *            all optional returns because the caller may, for example, be interested
 *            only in an optimized profile, or may only be interested in the HMM.
 *            
 *            Returns <eslENORESULT> if no consensus columns were annotated.
 *            Returns <eslEFORMAT> on MSA format problems, such as a missing RF annotation
 *            line in hand architecture construction. On any returned error,
 *            <bld->errbuf> contains an informative error message.
 *
 * Throws:    <eslEMEM> on allocation error.
 *            <eslEINVAL> if relative weights couldn't be calculated from <msa>.
 *
 * Xref:      J4/30.
 */
int
p7_Builder(P7_BUILDER *bld, ESL_MSA *msa, P7_BG *bg,
	   P7_HMM **opt_hmm, P7_TRACE ***opt_trarr, P7_PROFILE **opt_gm, P7_OPROFILE **opt_om,
	   ESL_MSA **opt_postmsa)
{
  int i,j;
  uint32_t    checksum = 0;	/* checksum calculated for the input MSA. hmmalign --mapali verifies against this. */
  P7_HMM     *hmm      = NULL;
  P7_TRACE  **tr       = NULL;
  P7_TRACE ***tr_ptr   = (opt_trarr != NULL || opt_postmsa != NULL) ? &tr : NULL;
  int         status;
  if ((status =  validate_msa         (bld, msa))                       != eslOK) goto ERROR;
  if ((status =  esl_msa_Checksum     (msa, &checksum))                 != eslOK) ESL_XFAIL(status, bld->errbuf, "Failed to calculate checksum"); 
  if ((status =  relative_weights     (bld, msa))                       != eslOK) goto ERROR;
  if ((status =  esl_msa_MarkFragments(msa, bld->fragthresh))           != eslOK) goto ERROR;
  if ((status =  build_model          (bld, msa, &hmm, tr_ptr))         != eslOK) goto ERROR;

  //Ensures that the weighted-average I->I count <=  bld->max_insert_len
  //(MI currently contains the number of observed insert-starts)
  if (bld->max_insert_len>0)
    for (i=1; i<hmm->M; i++ )
      hmm->t[i][p7H_II] = ESL_MIN(hmm->t[i][p7H_II], bld->max_insert_len*hmm->t[i][p7H_MI]);

  if ((status =  effective_seqnumber  (bld, msa, hmm, bg))              != eslOK) goto ERROR;
  if ((status =  parameterize         (bld, hmm))                       != eslOK) goto ERROR;
  if ((status =  annotate             (bld, msa, hmm))                  != eslOK) goto ERROR;
  if ((status =  calibrate            (bld, hmm, bg, opt_gm, opt_om))   != eslOK) goto ERROR;
  if ((status =  make_post_msa        (bld, msa, hmm, tr, opt_postmsa)) != eslOK) goto ERROR;

  //force masked positions to background  (it'll be close already, so no relevant impact on weighting)
  if (hmm->mm != NULL)
    for (i=1; i<hmm->M; i++ )
      if (hmm->mm[i] == 'm')
        for (j=0; j<hmm->abc->K; j++)
          hmm->mat[i][j] = bg->f[j];

  if ( bld->abc->type == eslDNA ||  bld->abc->type == eslRNA ) {
	  if (bld->w_len > 0)           hmm->max_length = bld->w_len;
	  else if (bld->w_beta == 0.0)  hmm->max_length = hmm->M *4;
	  else if ( (status =  p7_Builder_MaxLength(hmm, bld->w_beta)) != eslOK) goto ERROR;
  }

  hmm->checksum = checksum;
  hmm->flags   |= p7H_CHKSUM;

  if (opt_hmm   != NULL) *opt_hmm   = hmm; else p7_hmm_Destroy(hmm);
  if (opt_trarr != NULL) *opt_trarr = tr;  else p7_trace_DestroyArray(tr, msa->nseq);
  return eslOK;

 ERROR:
  p7_hmm_Destroy(hmm);
  p7_trace_DestroyArray(tr, msa->nseq);
  if (opt_gm    != NULL) p7_profile_Destroy(*opt_gm);
  if (opt_om    != NULL) p7_oprofile_Destroy(*opt_om);
  return status;
}

static void
utest_oprofileSendRecv(int my_rank, int nproc)
{
  ESL_RANDOMNESS *r    = esl_randomness_CreateFast(42);
  ESL_ALPHABET   *abc  = esl_alphabet_Create(eslAMINO);
  P7_HMM         *hmm  = NULL;
  P7_BG          *bg   = NULL;
  P7_PROFILE     *gm   = NULL;
  P7_OPROFILE    *om   = NULL;
  P7_OPROFILE    *om2  = NULL;
  int             M    = 200;
  int             L    = 400;
  char           *wbuf = NULL;
  int             wn   = 0;
  int             i;
  char            errbuf[eslERRBUFSIZE];

  p7_hmm_Sample(r, M, abc, &hmm); /* master and worker's sampled profiles are identical */
  bg = p7_bg_Create(abc);
  gm = p7_profile_Create(hmm->M, abc);
  om = p7_oprofile_Create(hmm->M, abc);
  p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL);
  p7_oprofile_Convert(gm, om);
  p7_bg_SetLength  (bg, L);

  if (my_rank == 0)
    {
      for (i = 1; i < nproc; i++)
	{
	  ESL_DPRINTF1(("Master: receiving test profile\n"));
	  p7_oprofile_MPIRecv(MPI_ANY_SOURCE, 0, MPI_COMM_WORLD, &wbuf, &wn, &abc, &om2);
	  ESL_DPRINTF1(("Master: test profile received\n"));

	  if (p7_oprofile_Compare(om, om2, 0.001, errbuf) != eslOK) 
	    p7_Die("Received profile not identical to what was sent\n%s", errbuf);

	  p7_oprofile_Destroy(om2);
	}
    }
  else 
    {
      ESL_DPRINTF1(("Worker %d: sending test profile\n", my_rank));
      p7_oprofile_MPISend(om, 0, 0, MPI_COMM_WORLD, &wbuf, &wn);
      ESL_DPRINTF1(("Worker %d: test profile sent\n", my_rank));
    }

  free(wbuf);
  p7_profile_Destroy(gm);
  p7_oprofile_Destroy(om);
  p7_bg_Destroy(bg);
  p7_hmm_Destroy(hmm);
  esl_alphabet_Destroy(abc);
  esl_randomness_Destroy(r);
  return;
}

/* 
 * compare to GForward() scores.
 */
static void
utest_fwdback(ESL_RANDOMNESS *r, ESL_ALPHABET *abc, P7_BG *bg, int M, int L, int N)
{
  char        *msg = "forward/backward unit test failed";
  P7_HMM      *hmm = NULL;
  P7_PROFILE  *gm  = NULL;
  P7_OPROFILE *om  = NULL;
  ESL_DSQ     *dsq = malloc(sizeof(ESL_DSQ) * (L+2));
  P7_OMX      *fwd = p7_omx_Create(M, 0, L);
  P7_OMX      *bck = p7_omx_Create(M, 0, L);
  P7_OMX      *oxf = p7_omx_Create(M, L, L);
  P7_OMX      *oxb = p7_omx_Create(M, L, L);
  P7_GMX      *gx  = p7_gmx_Create(M, L);
  float tolerance;
  float fsc1, fsc2;
  float bsc1, bsc2;
  float generic_sc;

  p7_FLogsumInit();
  if (p7_FLogsumError(-0.4, -0.5) > 0.0001) tolerance = 1.0;  /* weaker test against GForward()   */
  else tolerance = 0.0001;   /* stronger test: FLogsum() is in slow exact mode. */

  p7_oprofile_Sample(r, abc, bg, M, L, &hmm, &gm, &om);
  while (N--)
    {
      esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);

      p7_Forward       (dsq, L, om, oxf,      &fsc1);
      p7_Backward      (dsq, L, om, oxf, oxb, &bsc1);
      p7_ForwardParser (dsq, L, om, fwd,      &fsc2);
      p7_BackwardParser(dsq, L, om, fwd, bck, &bsc2);
      p7_GForward      (dsq, L, gm, gx,  &generic_sc);

      /* Forward and Backward scores should agree with high tolerance */
      if (fabs(fsc1-bsc1) > 0.0001)    esl_fatal(msg);
      if (fabs(fsc2-bsc2) > 0.0001)    esl_fatal(msg);
      if (fabs(fsc1-fsc2) > 0.0001)    esl_fatal(msg);

      /* GForward scores should approximate Forward scores, 
       * with tolerance that depends on how logsum.c was compiled
       */
      if (fabs(fsc1-generic_sc) > tolerance) esl_fatal(msg);
    }

  free(dsq);
  p7_hmm_Destroy(hmm);
  p7_omx_Destroy(oxb);
  p7_omx_Destroy(oxf);
  p7_omx_Destroy(bck);
  p7_omx_Destroy(fwd);
  p7_gmx_Destroy(gx);
  p7_profile_Destroy(gm);
  p7_oprofile_Destroy(om);
}

/* The Config test simply makes sure a random profile passes
 * a Validate() check.
 */
static void
utest_Config(P7_HMM *hmm, P7_BG *bg)
{
  char       *msg = "modelconfig.c::p7_ProfileConfig() unit test failed";
  P7_PROFILE *gm  = NULL;

  if ((gm = p7_profile_Create(hmm->M, hmm->abc))    == NULL)   esl_fatal(msg);
  if (p7_ProfileConfig(hmm, bg, gm, 350, p7_LOCAL)  != eslOK)  esl_fatal(msg);
  if (p7_profile_Validate(gm, NULL, 0.0001)         != eslOK)  esl_fatal(msg);

  p7_profile_Destroy(gm);
  return;
}

static void
emit_sequences(ESL_GETOPTS *go, FILE *ofp, int outfmt, ESL_RANDOMNESS *r, P7_HMM *hmm)
{
  ESL_SQ     *sq           = NULL;
  P7_TRACE   *tr           = NULL;
  P7_BG      *bg           = NULL;
  P7_PROFILE *gm           = NULL;
  int         do_profile   = esl_opt_GetBoolean(go, "-p");
  int         N            = esl_opt_GetInteger(go, "-N");
  int         L            = esl_opt_GetInteger(go, "-L");
  int         mode         = p7_LOCAL;
  int         nseq;
  int         status;

  if      (esl_opt_GetBoolean(go, "--local"))     mode = p7_LOCAL;
  else if (esl_opt_GetBoolean(go, "--unilocal"))  mode = p7_UNILOCAL;
  else if (esl_opt_GetBoolean(go, "--glocal"))    mode = p7_GLOCAL;
  else if (esl_opt_GetBoolean(go, "--uniglocal")) mode = p7_UNIGLOCAL;

  if ((sq = esl_sq_CreateDigital(hmm->abc))      == NULL)  esl_fatal("failed to allocate sequence");
  if ((tr = p7_trace_Create())                   == NULL)  esl_fatal("failed to allocate trace");
  if ((bg = p7_bg_Create(hmm->abc))              == NULL)  esl_fatal("failed to create null model");
  if ((gm = p7_profile_Create(hmm->M, hmm->abc)) == NULL)  esl_fatal("failed to create profile");

  if (p7_ProfileConfig(hmm, bg, gm, L, mode)     != eslOK) esl_fatal("failed to configure profile");
  if (p7_bg_SetLength(bg, L)                     != eslOK) esl_fatal("failed to reconfig null model length");
  if (p7_hmm_Validate    (hmm, NULL, 0.0001)     != eslOK) esl_fatal("whoops, HMM is bad!");
  if (p7_profile_Validate(gm,  NULL, 0.0001)     != eslOK) esl_fatal("whoops, profile is bad!");

  for (nseq = 1; nseq <= N; nseq++)
    {
      if (do_profile) status = p7_ProfileEmit(r, hmm, gm, bg, sq, tr);
      else            status = p7_CoreEmit   (r, hmm, sq, tr);
      if (status)  esl_fatal("Failed to emit sequence\n");

      status = esl_sq_FormatName(sq, "%s-sample%d", hmm->name, nseq);
      if (status) esl_fatal("Failed to set sequence name\n");

      status = esl_sqio_Write(ofp, sq, outfmt, FALSE);
      if (status != eslOK) esl_fatal("Failed to write sequence\n");

      p7_trace_Reuse(tr);
      esl_sq_Reuse(sq);
    }

  esl_sq_Destroy(sq);
  p7_trace_Destroy(tr);
  p7_bg_Destroy(bg);
  p7_profile_Destroy(gm);
  return;
}

/* compare results to GDecoding(). */
static void
utest_null2_expectation(ESL_RANDOMNESS *r, ESL_ALPHABET *abc, P7_BG *bg, int M, int L, int N, float tolerance)
{
  char        *msg  = "decoding unit test failed";
  P7_HMM      *hmm  = NULL;
  P7_PROFILE  *gm   = NULL;
  P7_OPROFILE *om   = NULL;
  ESL_DSQ     *dsq  = malloc(sizeof(ESL_DSQ) * (L+2));
  P7_OMX      *fwd  = p7_omx_Create(M, L, L);
  P7_OMX      *bck  = p7_omx_Create(M, L, L);
  P7_OMX      *pp   = p7_omx_Create(M, L, L);
  P7_GMX      *gxf  = p7_gmx_Create(M, L);
  P7_GMX      *gxb  = p7_gmx_Create(M, L);
  P7_GMX      *gpp  = p7_gmx_Create(M, L);
  float       *on2  = malloc(sizeof(float) * abc->Kp);
  float       *gn2  = malloc(sizeof(float) * abc->Kp);
  float fsc1, fsc2;
  float bsc1, bsc2;

  if (!gn2 || !on2) esl_fatal(msg);

  if (p7_oprofile_Sample(r, abc, bg, M, L, &hmm, &gm, &om) != eslOK) esl_fatal(msg);
  while (N--)
    {
      if (esl_rsq_xfIID(r, bg->f, abc->K, L, dsq) != eslOK) esl_fatal(msg);
      if (p7_Forward       (dsq, L, om, fwd,      &fsc1) != eslOK) esl_fatal(msg);
      if (p7_Backward      (dsq, L, om, fwd, bck, &bsc1) != eslOK) esl_fatal(msg);
      if (p7_Decoding(om, fwd, bck, pp)                  != eslOK) esl_fatal(msg);
      if (p7_Null2_ByExpectation(om, pp, on2)            != eslOK) esl_fatal(msg);
      
      if (p7_GForward (dsq, L, gm, gxf, &fsc2)           != eslOK) esl_fatal(msg);
      if (p7_GBackward(dsq, L, gm, gxb, &bsc2)           != eslOK) esl_fatal(msg);
      if (p7_GDecoding(gm, gxf, gxb, gpp)                != eslOK) esl_fatal(msg);
      if (p7_GNull2_ByExpectation(gm, gpp, gn2)          != eslOK) esl_fatal(msg);

      if (esl_vec_FCompare(gn2, on2, abc->Kp, tolerance) != eslOK) esl_fatal(msg);
    }

  p7_gmx_Destroy(gpp);
  p7_gmx_Destroy(gxf);
  p7_gmx_Destroy(gxb);
  p7_omx_Destroy(pp);
  p7_omx_Destroy(fwd);
  p7_omx_Destroy(bck);
  free(on2);
  free(gn2);
  free(dsq);
  p7_oprofile_Destroy(om);
  p7_profile_Destroy(gm);
  p7_hmm_Destroy(hmm);
}

/* Function:  p7_profile_Clone()
 * Synopsis:  Duplicates a profile.
 *
 * Purpose:   Duplicate profile <gm>; return a pointer
 *            to the newly allocated copy.
 *            
 * Returns:   ptr to new clone.
 * 
 * Throws:    <NULL> on allocation failure.
 */
P7_PROFILE *
p7_profile_Clone(const P7_PROFILE *gm)
{
  P7_PROFILE *g2 = NULL;
  int         status;

  if ((g2 = p7_profile_Create(gm->allocM, gm->abc)) == NULL) return NULL;
  if ((status = p7_profile_Copy(gm, g2)) != eslOK) goto ERROR;
  return g2;
  
 ERROR:
  p7_profile_Destroy(g2);
  return NULL;
}

/* Function:  p7_oprofile_Copy()
 * Synopsis:  Allocate an optimized profile structure.
 * Incept:    MSF Tue Nov 3, 2009 [Janelia]
 *
 * Purpose:   Allocate for profiles of up to <allocM> nodes for digital alphabet <abc>.
 *
 * Throws:    <NULL> on allocation error.
 */
P7_OPROFILE *
p7_oprofile_Copy(P7_OPROFILE *om1)
{
  P7_PROFILE  *dst   = NULL;

  if ((dst = p7_profile_Create(om1->M, om1->abc)) == NULL)  goto ERROR;
  if ((p7_profile_Copy(om1, dst))                 != eslOK) goto ERROR;
    
  return dst;

 ERROR:
  p7_profile_Destroy(dst);
  return NULL;
}

/* compare results to GDecoding(). */
static void
utest_decoding(ESL_RANDOMNESS *r, ESL_ALPHABET *abc, P7_BG *bg, int M, int L, int N, float tolerance)
{
  char        *msg  = "decoding unit test failed";
  P7_HMM      *hmm  = NULL;
  P7_PROFILE  *gm   = NULL;
  P7_OPROFILE *om   = NULL;
  ESL_DSQ     *dsq  = malloc(sizeof(ESL_DSQ) * (L+2));
  P7_OMX      *fwd  = p7_omx_Create(M, L, L);
  P7_OMX      *bck  = p7_omx_Create(M, L, L);
  P7_OMX      *pp   = p7_omx_Create(M, L, L);
  P7_GMX      *gxf  = p7_gmx_Create(M, L);
  P7_GMX      *gxb  = p7_gmx_Create(M, L);
  P7_GMX      *gxp1 = p7_gmx_Create(M, L);
  P7_GMX      *gxp2 = p7_gmx_Create(M, L);
  float fsc1, fsc2;
  float bsc1, bsc2;

  if (p7_oprofile_Sample(r, abc, bg, M, L, &hmm, &gm, &om) != eslOK) esl_fatal(msg);
  while (N--)
    {
      if (esl_rsq_xfIID(r, bg->f, abc->K, L, dsq) != eslOK) esl_fatal(msg);
      if (p7_Forward       (dsq, L, om, fwd,      &fsc1) != eslOK) esl_fatal(msg);
      if (p7_Backward      (dsq, L, om, fwd, bck, &bsc1) != eslOK) esl_fatal(msg);
      if (p7_Decoding(om, fwd, bck, pp)                  != eslOK) esl_fatal(msg);
      if (p7_omx_FDeconvert(pp, gxp1)                    != eslOK) esl_fatal(msg);
      
      if (p7_GForward (dsq, L, gm, gxf, &fsc2)           != eslOK) esl_fatal(msg);
      if (p7_GBackward(dsq, L, gm, gxb, &bsc2)           != eslOK) esl_fatal(msg);
      if (p7_GDecoding(gm, gxf, gxb, gxp2)               != eslOK) esl_fatal(msg);

      // p7_gmx_Dump(stdout, gxp1, p7_DEFAULT);
      // p7_gmx_Dump(stdout, gxp2, p7_DEFAULT);

      if (p7_gmx_Compare(gxp1, gxp2, tolerance)          != eslOK) esl_fatal(msg);
    }

  p7_gmx_Destroy(gxp1);
  p7_gmx_Destroy(gxp2);
  p7_gmx_Destroy(gxf);
  p7_gmx_Destroy(gxb);
  p7_omx_Destroy(fwd);
  p7_omx_Destroy(bck);
  p7_omx_Destroy(pp);
  free(dsq);
  p7_oprofile_Destroy(om);
  p7_profile_Destroy(gm);
  p7_hmm_Destroy(hmm);
}

/* Function:  p7_SingleBuilder()
 * Synopsis:  Build a new HMM from a single sequence.
 *
 * Purpose:   Take the sequence <sq> and a build configuration <bld>, and
 *            build a new HMM.
 *            
 *            The single sequence scoring system in the <bld>
 *            configuration must have been previously initialized by
 *            <p7_builder_SetScoreSystem()>.
 *            
 * Args:      bld       - build configuration
 *            sq        - query sequence
 *            bg        - null model (needed to paramaterize insert emission probs)
 *            opt_hmm   - optRETURN: new HMM
 *            opt_gm    - optRETURN: profile corresponding to <hmm>
 *            opt_om    - optRETURN: optimized profile corresponding to <gm>
 *
 * Returns:   <eslOK> on success.
 *
 * Throws:    <eslEMEM> on allocation error.
 *            <eslEINVAL> if <bld> isn't properly configured somehow.
 */
int
p7_SingleBuilder(P7_BUILDER *bld, ESL_SQ *sq, P7_BG *bg, P7_HMM **opt_hmm,
		 P7_TRACE **opt_tr, P7_PROFILE **opt_gm, P7_OPROFILE **opt_om)
{
  P7_HMM   *hmm = NULL;
  P7_TRACE *tr  = NULL;
  int       k;
  int       status;
  
  bld->errbuf[0] = '\0';
  if (! bld->Q) ESL_XEXCEPTION(eslEINVAL, "score system not initialized");

  if ((status = p7_Seqmodel(bld->abc, sq->dsq, sq->n, sq->name, bld->Q, bg->f, bld->popen, bld->pextend, &hmm)) != eslOK) goto ERROR;
  if ((status = p7_hmm_SetComposition(hmm))                                                                     != eslOK) goto ERROR;
  if ((status = p7_hmm_SetConsensus(hmm, sq))                                                                   != eslOK) goto ERROR; 
  if ((status = calibrate(bld, hmm, bg, opt_gm, opt_om))                                                        != eslOK) goto ERROR;

  if ( bld->abc->type == eslDNA ||  bld->abc->type == eslRNA ) {
    if (bld->w_len > 0)           hmm->max_length = bld->w_len;
    else if (bld->w_beta == 0.0)  hmm->max_length = hmm->M *4;
    else if ( (status =  p7_Builder_MaxLength(hmm, bld->w_beta)) != eslOK) goto ERROR;
  }


  /* build a faux trace: relative to core model (B->M_1..M_L->E) */
  if (opt_tr != NULL) 
    {
      if ((tr = p7_trace_Create())                      == NULL)  goto ERROR;
      if ((status = p7_trace_Append(tr, p7T_B, 0, 0))   != eslOK) goto ERROR; 
      for (k = 1; k <= sq->n; k++)
        if ((status = p7_trace_Append(tr, p7T_M, k, k)) != eslOK) goto ERROR;
      if ((status = p7_trace_Append(tr, p7T_E, 0, 0))   != eslOK) goto ERROR; 
      tr->M = sq->n;
      tr->L = sq->n;
    }

  /* note that <opt_gm> and <opt_om> were already set by calibrate() call above. */
  if (opt_hmm   != NULL) *opt_hmm = hmm; else p7_hmm_Destroy(hmm);
  if (opt_tr    != NULL) *opt_tr  = tr;
  return eslOK;

 ERROR:
  p7_hmm_Destroy(hmm);
  if (tr        != NULL) p7_trace_Destroy(tr);
  if (opt_gm    != NULL) p7_profile_Destroy(*opt_gm);
  if (opt_om    != NULL) p7_oprofile_Destroy(*opt_om);
  return status;
}

void destroy_hmmer_wrapper() {
  int index;
  if(models != NULL) {
    for(index = 0;index < num_models;index++) {
      p7_oprofile_Destroy(models[index]);
      p7_profile_Destroy(gmodels[index]);
    }
    free(models);
    free(gmodels);
  }

  if(wrapper_result