Files hmmer-2.3.2-original/squid/libsquid.a and hmmer-2.3.2/squid/libsquid.a differ
diff -uNr hmmer-2.3.2-original/src/fast_algorithms.c hmmer-2.3.2/src/fast_algorithms.c
--- hmmer-2.3.2-original/src/fast_algorithms.c	2003-10-04 15:01:08.000000000 -0400
+++ hmmer-2.3.2/src/fast_algorithms.c	2006-05-02 22:58:02.418721750 -0400
@@ -82,6 +82,8 @@
   int  *dpp;                 /* ptr into dmx[i-1] (previous row) */
   int  *tpmm, *tpmi, *tpmd, *tpim, *tpii, *tpdm, *tpdd; /* ptrs into tsc */
   int   M;
+  /* JL changes to break some inter-line dependencies */
+  int  sc1,sc2,sc3,sc4,sc5,sc6,sc7,sc8;
   
   /* Make sure we have space for a DP matrix with 0..L rows, 0..M-1 columns.
    */ 
@@ -127,61 +129,84 @@
     dc[0] = -INFTY;
     ic[0] = -INFTY;
 
-    for (k = 1; k <= M; k++) {
-      mc[k] = mpp[k-1]   + tpmm[k-1];
-      if ((sc = ip[k-1]  + tpim[k-1]) > mc[k])  mc[k] = sc;
-      if ((sc = dpp[k-1] + tpdm[k-1]) > mc[k])  mc[k] = sc;
-      if ((sc = xmb  + bp[k])         > mc[k])  mc[k] = sc; 
-      mc[k] += ms[k];
-      if (mc[k] < -INFTY) mc[k] = -INFTY;  
-
-      dc[k] = dc[k-1] + tpdd[k-1];
-      if ((sc = mc[k-1] + tpmd[k-1]) > dc[k]) dc[k] = sc;
-      if (dc[k] < -INFTY) dc[k] = -INFTY;  
-
-      if (k < M) {
-	ic[k] = mpp[k] + tpmi[k];
-	if ((sc = ip[k] + tpii[k]) > ic[k]) ic[k] = sc; 
-	ic[k] += is[k];
-	if (ic[k] < -INFTY) ic[k] = -INFTY; 
-      }
+    for (k = 1; k < M; k++) {
+      /* mc[k] = mpp[k-1]   + tpmm[k-1]; */
+      sc1 = mpp[k-1]   + tpmm[k-1];
+      if (( ip[k-1]  + tpim[k-1]) > sc1)  sc1 = ip[k-1]  + tpim[k-1] ;
+      if (( dpp[k-1] + tpdm[k-1]) > sc1)  sc1 = dpp[k-1] + tpdm[k-1] ;
+      if (( xmb  + bp[k])         > sc1)  sc1 = xmb  + bp[k] ; 
+      sc1 += ms[k];
+      if (sc1 < -INFTY) sc1 = -INFTY;
+      mc[k] = sc1;  
+    }
+    
+    for (k = 1; k < M; k++) {    
+      /* dc[k] = dc[k-1] + tpdd[k-1]; */
+      sc2 = dc[k-1] + tpdd[k-1]; 
+      if (( mc[k-1] + tpmd[k-1]) > sc2) sc2 = mc[k-1] + tpmd[k-1] ;
+      if (sc2 < -INFTY) sc2 = -INFTY;  
+      dc[k] = sc2;
     }
 
+    for (k = 1; k < M; k++) {    
+      /* ic[k] = mpp[k] + tpmi[k]; */
+      sc3 = mpp[k] + tpmi[k];
+      if ((ip[k] + tpii[k]) > sc3) sc3 = ip[k] + tpii[k] ; 
+      sc3 += is[k];
+      if (sc3 < -INFTY) sc3 = -INFTY;     
+      ic[k]=sc3 ;
+    }
+    
+    k = M;
+    sc4 = mpp[k-1]   + tpmm[k-1];
+    if (( ip[k-1]  + tpim[k-1]) > sc4)  sc4 = ip[k-1]  + tpim[k-1] ;
+    if (( dpp[k-1] + tpdm[k-1]) > sc4)  sc4 = dpp[k-1] + tpdm[k-1] ;
+    if (( xmb  + bp[k])         > sc4)  sc4 = xmb  + bp[k] ; 
+    sc4 += ms[k];
+    if (sc4 < -INFTY) sc1 = -INFTY;
+    mc[k] = sc4;  
+
+    dc[k] = dc[k-1] + tpdd[k-1];
+    if (( mc[k-1] + tpmd[k-1]) > dc[k]) dc[k] = mc[k-1] + tpmd[k-1] ;
+    if (dc[k] < -INFTY) dc[k] = -INFTY;  
+    
+    
+
     /* Now the special states. Order is important here.
      * remember, C and J emissions are zero score by definition,
      */
 				/* N state */
     xmx[i][XMN] = -INFTY;
-    if ((sc = xmx[i-1][XMN] + hmm->xsc[XTN][LOOP]) > -INFTY)
-      xmx[i][XMN] = sc;
+    if (( xmx[i-1][XMN] + hmm->xsc[XTN][LOOP]) > -INFTY)
+      xmx[i][XMN] = xmx[i-1][XMN] + hmm->xsc[XTN][LOOP];
 
 				/* E state */
     xme = -INFTY;
     mpc = mmx[i];
     ep  = hmm->esc;
     for (k = 1; k <= hmm->M; k++)
-      if ((sc =  mpc[k] + ep[k]) > xme) xme = sc; 
+      if ((mpc[k] + ep[k]) > xme) xme = mpc[k] + ep[k] ; 
     xmx[i][XME] = xme;
 				/* J state */
     xmx[i][XMJ] = -INFTY;
-    if ((sc = xmx[i-1][XMJ] + hmm->xsc[XTJ][LOOP]) > -INFTY)
-      xmx[i][XMJ] = sc;
-    if ((sc = xmx[i][XME]   + hmm->xsc[XTE][LOOP]) > xmx[i][XMJ])
-      xmx[i][XMJ] = sc;
+    if (( xmx[i-1][XMJ] + hmm->xsc[XTJ][LOOP]) > -INFTY)
+      xmx[i][XMJ] = xmx[i-1][XMJ] + hmm->xsc[XTJ][LOOP];
+    if ((  xmx[i][XME]   + hmm->xsc[XTE][LOOP]) > xmx[i][XMJ])
+      xmx[i][XMJ] = xmx[i][XME]   + hmm->xsc[XTE][LOOP] ;
 
 				/* B state */
     xmx[i][XMB] = -INFTY;
-    if ((sc = xmx[i][XMN] + hmm->xsc[XTN][MOVE]) > -INFTY)
-      xmx[i][XMB] = sc;
-    if ((sc = xmx[i][XMJ] + hmm->xsc[XTJ][MOVE]) > xmx[i][XMB])
-      xmx[i][XMB] = sc;
+    if (( xmx[i][XMN] + hmm->xsc[XTN][MOVE]) > -INFTY)
+      xmx[i][XMB] = xmx[i][XMN] + hmm->xsc[XTN][MOVE];
+    if (( xmx[i][XMJ] + hmm->xsc[XTJ][MOVE]) > xmx[i][XMB])
+      xmx[i][XMB] = xmx[i][XMJ] + hmm->xsc[XTJ][MOVE];
 
 				/* C state */
     xmx[i][XMC] = -INFTY;
-    if ((sc = xmx[i-1][XMC] + hmm->xsc[XTC][LOOP]) > -INFTY)
-      xmx[i][XMC] = sc;
-    if ((sc = xmx[i][XME] + hmm->xsc[XTE][MOVE]) > xmx[i][XMC])
-      xmx[i][XMC] = sc;
+    if (( xmx[i-1][XMC] + hmm->xsc[XTC][LOOP]) > -INFTY)
+      xmx[i][XMC] = xmx[i-1][XMC] + hmm->xsc[XTC][LOOP];
+    if (( xmx[i][XME] + hmm->xsc[XTE][MOVE]) > xmx[i][XMC])
+      xmx[i][XMC] = xmx[i][XME] + hmm->xsc[XTE][MOVE];
   }
 				/* T state (not stored) */
   sc = xmx[L][XMC] + hmm->xsc[XTC][MOVE];
Files hmmer-2.3.2-original/testsuite/sreaa15511.OPT.HMM.ssi and hmmer-2.3.2/testsuite/sreaa15511.OPT.HMM.ssi differ