Description: rename binaries in man pages
 Binaries are renamed in man pages to match their new file names.
 .
 No need to forward this patch as it tackles issues with the way hmmer versions
 are packaged for Debian.
Author: Laszlo Kajan <lkajan@rostlab.org>
Forwarded: no

--- a/documentation/man/hmmer.man
+++ b/documentation/man/hmmer.man
@@ -1,4 +1,4 @@
-.TH "hmmer" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual"
+.TH "hmmer2" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual"
 
 .SH NAME
 .TP 
@@ -6,41 +6,41 @@
 
 .SH SYNOPSIS
 .TP
-.B hmmalign
+.B hmm2align
 Align multiple sequences to a profile HMM.
 
 .TP
-.B hmmbuild
+.B hmm2build
 Build a profile HMM from a given multiple sequence alignment.
 
 .TP
-.B hmmcalibrate
+.B hmm2calibrate
 Determine appropriate statistical significance parameters 
 for a profile HMM prior to doing database searches.
 
 .TP 
-.B hmmconvert
+.B hmm2convert
 Convert HMMER profile HMMs to other formats, such as GCG profiles.
 
 .TP
-.B hmmemit
+.B hmm2emit
 Generate sequences probabilistically from a profile HMM.
 
 .TP
-.B hmmfetch
+.B hmm2fetch
 Retrieve an HMM from an HMM database
 
 .TP 
-.B hmmindex
+.B hmm2index
 Create a binary SSI index for an HMM database
 
 .TP
-.B hmmpfam
+.B hmm2pfam
 Search a profile HMM database with a sequence (i.e., annotate various
 kinds of domains in the query sequence).
 
 .TP
-.B hmmsearch
+.B hmm2search
 Search a sequence database with a profile HMM (i.e., find additional
 homologues of a modeled family). 
 
--- a/documentation/man/hmmalign.man
+++ b/documentation/man/hmmalign.man
@@ -1,18 +1,18 @@
-.TH "hmmalign" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual"
+.TH "hmm2align" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual"
 
 .SH NAME
 .TP 
-hmmalign - align sequences to an HMM profile
+hmm2align - align sequences to an HMM profile
 
 .SH SYNOPSIS
-.B hmmalign
+.B hmm2align
 .I [options]
-.I hmmfile
+.I hmm2file
 .I seqfile
 
 .SH DESCRIPTION
 
-.B hmmalign
+.B hmm2align
 reads an HMM file from
 .I hmmfile
 and a set of sequences from 
@@ -26,7 +26,7 @@
 accepted by HMMER. If it is in a multiple alignment format
 (e.g. Stockholm, MSF, SELEX, ClustalW), the existing alignment
 is ignored (i.e., the sequences are read as if they were
-unaligned - hmmalign will align them the way it wants).
+unaligned - hmm2align will align them the way it wants).
 
 .SH OPTIONS
 
@@ -76,7 +76,7 @@
 .I <f> 
 is held fixed. 
 This allows you to align sequences to a model with 
-.B hmmalign
+.B hmm2align
 and view them in the context of an existing trusted
 multiple alignment. 
 The alignment to the alignment is defined by a "map" kept
@@ -110,7 +110,7 @@
 .I <f> 
 is held fixed.
 This allows you to align sequences to a model with 
-.B hmmalign
+.B hmm2align
 and view them in the context of an existing trusted
 multiple alignment. The alignment to the alignment is
 done with a heuristic (nonoptimal) dynamic programming procedure,
@@ -127,7 +127,7 @@
 
 Master man page, with full list of and guide to the individual man
 pages: see 
-.B hmmer(1).
+.B hmmer2(1).
 .PP
 For complete documentation, see the user guide that came with the
 distribution (Userguide.pdf); or see the HMMER web page,
--- a/documentation/man/hmmbuild.man
+++ b/documentation/man/hmmbuild.man
@@ -1,18 +1,18 @@
-.TH "hmmbuild" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual"
+.TH "hmm2build" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual"
 
 .SH NAME
 .TP 
-hmmbuild - build a profile HMM from an alignment
+hmm2build - build a profile HMM from an alignment
 
 .SH SYNOPSIS
-.B hmmbuild
+.B hmm2build
 .I [options]
 .I hmmfile
 .I alignfile
 
 .SH DESCRIPTION
 
-.B hmmbuild 
+.B hmm2build 
 reads a multiple sequence alignment file 
 .I alignfile
 , builds a new profile HMM, and saves the HMM in 
@@ -311,7 +311,7 @@
 weights (PB weights) are more efficient. At or above a certain
 threshold sequence number
 .I <n> 
-.B hmmbuild 
+.B hmm2build 
 will switch from GSC, BLOSUM, or Voronoi weights to
 PB weights. To disable this switching behavior (at the cost
 of compute time, set 
@@ -436,7 +436,7 @@
 
 Master man page, with full list of and guide to the individual man
 pages: see 
-.B hmmer(1).
+.B hmmer2(1).
 .PP
 For complete documentation, see the user guide that came with the
 distribution (Userguide.pdf); or see the HMMER web page,
--- a/documentation/man/hmmcalibrate.man
+++ b/documentation/man/hmmcalibrate.man
@@ -1,17 +1,17 @@
-.TH "hmmcalibrate" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual"
+.TH "hmm2calibrate" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual"
 
 .SH NAME
 .TP 
-hmmcalibrate - calibrate HMM search statistics
+hmm2calibrate - calibrate HMM search statistics
 
 .SH SYNOPSIS
-.B hmmcalibrate
+.B hmm2calibrate
 .I [options]
 .I hmmfile
 
 .SH DESCRIPTION
 
-.B hmmcalibrate
+.B hmm2calibrate
 reads an HMM file from
 .I hmmfile,
 scores a large number of synthesized random sequences with it, fits an
@@ -21,13 +21,13 @@
 now including the EVD parameters.
 
 .PP
-.B hmmcalibrate 
+.B hmm2calibrate 
 may take several minutes (or longer) to run.
 While it is running, a temporary file called
 .I hmmfile.xxx
 is generated in your working directory. 
 If you abort 
-.B hmmcalibrate 
+.B hmm2calibrate 
 prematurely (ctrl-C, for instance), your original
 .I hmmfile 
 will be untouched, and you should delete the
@@ -94,7 +94,7 @@
 .B --pvm
 Run on a Parallel Virtual Machine (PVM). The PVM must
 already be running. The client program 
-.B hmmcalibrate-pvm
+.B hmm2calibrate-pvm
 must be installed on all the PVM nodes.
 Optional PVM support must have been compiled into 
 HMMER. 
@@ -120,12 +120,12 @@
 .B time()
 to generate a different seed for each run, which
 means that two different runs of
-.B hmmcalibrate
+.B hmm2calibrate
 on the same HMM will give slightly different
 results.  You can use
 this option to generate reproducible results for
 different 
-.B hmmcalibrate 
+.B hmm2calibrate 
 runs on the same HMM.
 
 
@@ -133,7 +133,7 @@
 
 Master man page, with full list of and guide to the individual man
 pages: see 
-.B hmmer(1).
+.B hmmer2(1).
 .PP
 For complete documentation, see the user guide that came with the
 distribution (Userguide.pdf); or see the HMMER web page,
--- a/documentation/man/hmmconvert.man
+++ b/documentation/man/hmmconvert.man
@@ -1,18 +1,18 @@
-.TH "hmmconvert" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual"
+.TH "hmm2convert" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual"
 
 .SH NAME
 .TP 
-hmmconvert - convert between profile HMM file formats
+hmm2convert - convert between profile HMM file formats
 
 .SH SYNOPSIS
-.B hmmconvert
+.B hmm2convert
 .I [options]
 .I oldhmmfile
 .I newhmmfile
 
 .SH DESCRIPTION
 
-.B hmmconvert
+.B hmm2convert
 reads an HMM file from
 .I oldhmmfile
 in any HMMER format, and writes it to a new file
@@ -66,7 +66,7 @@
 already exists, and
 .I -A 
 is not being used to append to the file,
-hmmconvert will refuse to clobber the existing
+hmm2convert will refuse to clobber the existing
 file unless 
 .I -F 
 is used.
@@ -84,7 +84,7 @@
 
 Master man page, with full list of and guide to the individual man
 pages: see 
-.B hmmer(1).
+.B hmmer2(1).
 .PP
 For complete documentation, see the user guide that came with the
 distribution (Userguide.pdf); or see the HMMER web page,
--- a/documentation/man/hmmemit.man
+++ b/documentation/man/hmmemit.man
@@ -1,17 +1,17 @@
-.TH "hmmemit" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual"
+.TH "hmm2emit" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual"
 
 .SH NAME
 .TP 
-hmmemit - generate sequences from a profile HMM
+hmm2emit - generate sequences from a profile HMM
 
 .SH SYNOPSIS
-.B hmmemit
+.B hmm2emit
 .I [options]
 .I hmmfile
 
 .SH DESCRIPTION
 
-.B hmmemit
+.B hmm2emit
 reads an HMM file from
 .I hmmfile
 containing one or more HMMs,
@@ -22,9 +22,9 @@
 This can be useful for various applications in which one needs a simulation
 of sequences consistent with a sequence family consensus. 
 
-.pp
+.PP
 By default,
-.B hmmemit
+.B hmm2emit
 generates 10 sequences and outputs them in FASTA (unaligned) format.
 
 .SH OPTIONS
@@ -78,7 +78,7 @@
 .B time()
 to generate a different seed for each run, which
 means that two different runs of
-.B hmmemit
+.B hmm2emit
 on the same HMM will give slightly different
 results.  You can use
 this option to generate reproducible results.
@@ -89,7 +89,7 @@
 
 Master man page, with full list of and guide to the individual man
 pages: see 
-.B hmmer(1).
+.B hmmer2(1).
 .PP
 For complete documentation, see the user guide that came with the
 distribution (Userguide.pdf); or see the HMMER web page,
--- a/documentation/man/hmmfetch.man
+++ b/documentation/man/hmmfetch.man
@@ -1,18 +1,18 @@
-.TH "hmmfetch" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual"
+.TH "hmm2fetch" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual"
 
 .SH NAME
 .TP 
-hmmfetch - retrieve an HMM from an HMM database
+hmm2fetch - retrieve an HMM from an HMM database
 
 .SH SYNOPSIS
-.B hmmfetch
+.B hmm2fetch
 .I [options]
 .I database
 .I name
 
 .SH DESCRIPTION
 
-.B hmmfetch
+.B hmm2fetch
 is a small utility that retrieves an HMM called
 .I name
 from a HMMER model database called
@@ -20,7 +20,7 @@
 in a new format, 
 and prints that model to standard output.
 For example,
-.I hmmfetch Pfam rrm
+.I hmm2fetch Pfam rrm
 retrieves the RRM (RNA recognition motif) model from
 Pfam, if the environment variable HMMERDB is
 set to the location of the Pfam database.
@@ -29,7 +29,7 @@
 .PP
 The database must have an associated GSI index file.
 To index an HMM database, use the program
-.B hmmindex.
+.B hmm2index.
 
 .SH OPTIONS
 
@@ -47,14 +47,14 @@
 called
 .B foo,
 you would do 
-.B hmmfetch -n 0 foo.
+.B hmm2fetch -n 0 foo.
 
 
 .SH SEE ALSO
 
 Master man page, with full list of and guide to the individual man
 pages: see 
-.B hmmer(1).
+.B hmmer2(1).
 .PP
 For complete documentation, see the user guide that came with the
 distribution (Userguide.pdf); or see the HMMER web page,
--- a/documentation/man/hmmindex.man
+++ b/documentation/man/hmmindex.man
@@ -1,26 +1,26 @@
-.TH "hmmindex" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual"
+.TH "hmm2index" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual"
 
 .SH NAME
 .TP 
-hmmindex - create a binary SSI index for an HMM database
+hmm2index - create a binary SSI index for an HMM database
 
 .SH SYNOPSIS
-.B hmmindex
+.B hmm2index
 .I [options]
 .I database
 
 .SH DESCRIPTION
 
-.B hmmindex
+.B hmm2index
 is a utility that creates a binary SSI ("squid sequence index"
 format) index for an HMM database file called
 .I database.
 The new index file is named
 .IR database.ssi.
 An SSI index file is required for 
-.B hmmfetch
+.B hmm2fetch
 to work, and also for the PVM implementation of 
-.B hmmpfam.
+.B hmm2pfam.
 
 .SH OPTIONS
 
@@ -35,7 +35,7 @@
 
 Master man page, with full list of and guide to the individual man
 pages: see 
-.B hmmer(1).
+.B hmmer2(1).
 .PP
 For complete documentation, see the user guide that came with the
 distribution (Userguide.pdf); or see the HMMER web page,
--- a/documentation/man/hmmpfam.man
+++ b/documentation/man/hmmpfam.man
@@ -1,18 +1,18 @@
-.TH "hmmpfam" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual"
+.TH "hmm2pfam" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual"
 
 .SH NAME
 .TP
-hmmpfam - search one or more sequences against an HMM database
+hmm2pfam - search one or more sequences against an HMM database
 
 .SH SYNOPSIS
-.B hmmpfam
+.B hmm2pfam
 .I [options]
 .I hmmfile
 .I seqfile
 
 .SH DESCRIPTION
 
-.B hmmpfam
+.B hmm2pfam
 reads a sequence file
 .I seqfile
 and compares each sequence in it, one at a time, against all the HMMs in
@@ -65,7 +65,7 @@
 Specify that models and sequence are nucleic acid, not protein.
 Other HMMER programs autodetect this; but because of the order in
 which 
-.B hmmpfam
+.B hmm2pfam
 accesses data, it can't reliably determine the correct "alphabet"
 by itself.
 
@@ -134,7 +134,7 @@
 to --globT <GA1> --domT <GA2>, but the GA1 and GA2 cutoffs
 are read from each HMM in
 .I hmmfile
-individually. hmmbuild puts these cutoffs there
+individually. hmm2build puts these cutoffs there
 if the alignment file was annotated in a Pfam-friendly
 alignment format (extended SELEX or Stockholm format) and 
 the optional GA annotation line was present. If these
@@ -148,7 +148,7 @@
 to --globT <TC1> --domT <TC2>, but the TC1 and TC2 cutoffs
 are read from each HMM in
 .I hmmfile
-individually. hmmbuild puts these cutoffs there
+individually. hmm2build puts these cutoffs there
 if the alignment file was annotated in a Pfam-friendly
 alignment format (extended SELEX or Stockholm format) and 
 the optional TC annotation line was present. If these
@@ -162,7 +162,7 @@
 to --globT <NC1> --domT <NC2>, but the NC1 and NC2 cutoffs
 are read from each HMM in
 .I hmmfile
-individually. hmmbuild puts these cutoffs there
+individually. hmm2build puts these cutoffs there
 if the alignment file was annotated in a Pfam-friendly
 alignment format (extended SELEX or Stockholm format) and 
 the optional NC annotation line was present. If these
@@ -246,7 +246,7 @@
 .B --pvm
 Run on a Parallel Virtual Machine (PVM). The PVM must
 already be running. The client program 
-.B hmmpfam-pvm
+.B hmm2pfam-pvm
 must be installed on all the PVM nodes.
 The HMM database
 .I hmmfile
@@ -254,7 +254,7 @@
 .IR hmmfile. gsi
 must also be installed on all the PVM nodes.
 (The GSI index is produced by the program
-.BR hmmindex .)
+.BR hmm2index .)
 Because the PVM implementation is I/O bound,
 it is highly recommended that each node have a
 local copy of 
@@ -280,7 +280,7 @@
 
 Master man page, with full list of and guide to the individual man
 pages: see 
-.B hmmer(1).
+.B hmmer2(1).
 .PP
 For complete documentation, see the user guide that came with the
 distribution (Userguide.pdf); or see the HMMER web page,
--- a/documentation/man/hmmsearch.man
+++ b/documentation/man/hmmsearch.man
@@ -1,18 +1,18 @@
-.TH "hmmsearch" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual"
+.TH "hmm2search" 1 "Oct 2003" "HMMER 2.3.2" "HMMER Manual"
 
 .SH NAME
 .TP 
-hmmsearch - search a sequence database with a profile HMM
+hmm2search - search a sequence database with a profile HMM
 
 .SH SYNOPSIS
-.B hmmsearch
+.B hmm2search
 .I [options]
 .I hmmfile
 .I seqfile
 
 .SH DESCRIPTION
 
-.B hmmsearch
+.B hmm2search
 reads an HMM from
 .I hmmfile
 and searches 
@@ -28,7 +28,7 @@
 has been configured for the site.
 
 .PP
-.B hmmsearch
+.B hmm2search
 may take minutes or even hours to run, depending
 on the size of the sequence database. It is a good
 idea to redirect the output to a file.
@@ -121,7 +121,7 @@
 Use Pfam GA (gathering threshold) score cutoffs. 
 Equivalent
 to --globT <GA1> --domT <GA2>, but the GA1 and GA2 cutoffs
-are read from the HMM file. hmmbuild puts these cutoffs there
+are read from the HMM file. hmm2build puts these cutoffs there
 if the alignment file was annotated in a Pfam-friendly
 alignment format (extended SELEX or Stockholm format) and 
 the optional GA annotation line was present. If these
@@ -133,7 +133,7 @@
 .B --cut_tc
 Use Pfam TC (trusted cutoff) score cutoffs. Equivalent
 to --globT <TC1> --domT <TC2>, but the TC1 and TC2 cutoffs
-are read from the HMM file. hmmbuild puts these cutoffs there
+are read from the HMM file. hmm2build puts these cutoffs there
 if the alignment file was annotated in a Pfam-friendly
 alignment format (extended SELEX or Stockholm format) and 
 the optional TC annotation line was present. If these
@@ -145,7 +145,7 @@
 .B --cut_nc
 Use Pfam NC (noise cutoff) score cutoffs. Equivalent
 to --globT <NC1> --domT <NC2>, but the NC1 and NC2 cutoffs
-are read from the HMM file. hmmbuild puts these cutoffs there
+are read from the HMM file. hmm2build puts these cutoffs there
 if the alignment file was annotated in a Pfam-friendly
 alignment format (extended SELEX or Stockholm format) and 
 the optional NC annotation line was present. If these
@@ -229,7 +229,7 @@
 .B --pvm
 Run on a Parallel Virtual Machine (PVM). The PVM must
 already be running. The client program 
-.B hmmsearch-pvm
+.B hmm2search-pvm
 must be installed on all the PVM nodes.
 Optional PVM support must have been compiled into 
 HMMER.
@@ -247,7 +247,7 @@
 
 Master man page, with full list of and guide to the individual man
 pages: see 
-.B hmmer(1).
+.B hmmer2(1).
 .PP
 For complete documentation, see the user guide that came with the
 distribution (Userguide.pdf); or see the HMMER web page,
