From: Michael R. Crusoe <crusoe@debian.org>
Subject: fix a typo
Forwarded: https://github.com/EddyRivasLab/hmmer/pull/217

--- hmmer.orig/src/nhmmer.c
+++ hmmer/src/nhmmer.c
@@ -343,7 +343,7 @@
 
 #if defined (eslENABLE_SSE)
   if (esl_opt_IsUsed(go, "--seed_max_depth")    && fprintf(ofp, "# FM Seed length:                  %d\n",             esl_opt_GetInteger(go, "--seed_max_depth"))    < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
-  if (esl_opt_IsUsed(go, "--seed_sc_thresh")    && fprintf(ofp, "# FM score threshhold (bits):      %g\n",             esl_opt_GetReal(go, "--seed_sc_thresh"))    < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
+  if (esl_opt_IsUsed(go, "--seed_sc_thresh")    && fprintf(ofp, "# FM score threshold (bits):       %g\n",             esl_opt_GetReal(go, "--seed_sc_thresh"))    < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
   if (esl_opt_IsUsed(go, "--seed_sc_density")   && fprintf(ofp, "# FM score density (bits/pos):     %g\n",             esl_opt_GetReal(go, "--seed_sc_density"))        < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
   if (esl_opt_IsUsed(go, "--seed_drop_max_len") && fprintf(ofp, "# FM max neg-growth length:        %d\n",             esl_opt_GetInteger(go, "--seed_drop_max_len")) < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
   if (esl_opt_IsUsed(go, "--seed_drop_lim")     && fprintf(ofp, "# FM max run drop:                 %g\n",             esl_opt_GetReal(go, "--seed_drop_lim"))        < 0) ESL_EXCEPTION_SYS(eslEWRITE, "write failed");
--- hmmer.orig/documentation/man/alimask.man.in
+++ hmmer/documentation/man/alimask.man.in
@@ -219,7 +219,7 @@
 .TP 
 .B \-\-wblosum
 Use the same clustering scheme that was used to weight data in
-calculating BLOSUM subsitution matrices [Henikoff and Henikoff,
+calculating BLOSUM substitution matrices [Henikoff and Henikoff,
 Proc. Natl. Acad. Sci 89:10915, 1992]. Sequences are single-linkage
 clustered at an identity threshold (default 0.62; see
 .BR \-\-wid )
--- hmmer.orig/documentation/man/hmmbuild.man.in
+++ hmmer/documentation/man/hmmbuild.man.in
@@ -177,7 +177,7 @@
 .TP 
 .B \-\-wblosum
 Use the same clustering scheme that was used to weight data in
-calculating BLOSUM subsitution matrices [Henikoff and Henikoff,
+calculating BLOSUM substitution matrices [Henikoff and Henikoff,
 Proc. Natl. Acad. Sci 89:10915, 1992]. Sequences are single-linkage
 clustered at an identity threshold (default 0.62; see
 .BR \-\-wid )
--- hmmer.orig/documentation/man/jackhmmer.man.in
+++ hmmer/documentation/man/jackhmmer.man.in
@@ -492,7 +492,7 @@
 .TP 
 .B \-\-wblosum
 Use the same clustering scheme that was used to weight data in
-calculating BLOSUM subsitution matrices [Henikoff and Henikoff,
+calculating BLOSUM substitution matrices [Henikoff and Henikoff,
 Proc. Natl. Acad. Sci 89:10915, 1992]. Sequences are single-linkage
 clustered at an identity threshold (default 0.62; see
 .BR \-\-wid )
--- hmmer.orig/documentation/userguide/introduction.tex
+++ hmmer/documentation/userguide/introduction.tex
@@ -77,7 +77,7 @@
 multiple sequence alignment.
 
 Pairwise sequence alignment methods such as BLAST and FASTA use
-position-\emph{independent} subsitution score matrices such as BLOSUM
+position-\emph{independent} substitution score matrices such as BLOSUM
 and PAM, but the desirability of position-\emph{specific} models was
 recognized even before BLAST and FASTA were written.\cite{Doolittle81}
 Several groups introduced different position-specific alignment
--- hmmer.orig/easel/esl_ratematrix.c
+++ hmmer/easel/esl_ratematrix.c
@@ -398,7 +398,7 @@
  *
  * Args:      Q     - rate matrix to normalize
  *            pi    - stationary residue frequencies
- *            unit  - expected subsitution rate per dt 
+ *            unit  - expected substitution rate per dt 
  *                    (1.0 = substitutions/site; 0.01 = PAMs)
  *
  * Returns:   <eslOK> on success, and matrix Q is rescaled.
--- hmmer.orig/easel/esl_ratematrix.tex
+++ hmmer/easel/esl_ratematrix.tex
@@ -1,3 +1,3 @@
 The \eslmod{ratematrix} module implements continuous-time Markov
-evolutionary models of residue subsitution.
+evolutionary models of residue substitution.
 
--- hmmer.orig/documentation/man/nhmmer.man.in
+++ hmmer/documentation/man/nhmmer.man.in
@@ -509,7 +509,7 @@
 .BR stockholm
 format, the
 .BR \-\-qsingle_seqs
- flag will cause each sequence in that alignment to be used as a seperate query sequence.
+ flag will cause each sequence in that alignment to be used as a separate query sequence.
 
 .TP
 .BI \-\-tformat " <s>"
--- hmmer.orig/easel/miniapps/esl-alimask.c
+++ hmmer/easel/miniapps/esl-alimask.c
@@ -169,7 +169,7 @@
       puts("\n  Only one usage listed above can be used per execution with the exception of");
       puts("  -p and -g, which can be used in combination with each other.\n");
       puts("  With -t, <coords> is a string that specifies positive integer start and end");
-      puts("  coordinates seperated by any nonnumeric, nonspace character(s).");
+      puts("  coordinates separated by any nonnumeric, nonspace character(s).");
       puts("  For example, \"23..100\" or \"23/100\" or \"23-100\" all specify that columns");
       puts("  23 to 100 be kept and all other columns be removed. Additionally, to retrieve");
       puts("  all columns from a position to the end, omit the end coord; \"23:\" will work.");
