[med-svn] r18726 - trunk/packages/vsearch/trunk/debian/patches

Mon Feb 2 09:40:51 UTC 2015

Author: tille
Date: 2015-02-02 09:40:50 +0000 (Mon, 02 Feb 2015)
New Revision: 18726

Modified:
   trunk/packages/vsearch/trunk/debian/patches/manpage_syntax.patch
Log:
More manpage syntax issues fixed


Modified: trunk/packages/vsearch/trunk/debian/patches/manpage_syntax.patch
===================================================================

--- trunk/packages/vsearch/trunk/debian/patches/manpage_syntax.patch	2015-02-02 09:01:35 UTC (rev 18725)
+++ trunk/packages/vsearch/trunk/debian/patches/manpage_syntax.patch	2015-02-02 09:40:50 UTC (rev 18726)
@@ -79,3 +79,1227 @@
  \fIoutputfile\fR [\fIoptions\fR]
  .PP
  .RE
+@@ -107,10 +107,10 @@ present. All other ascii or non-ascii ch
+ complained about in a non-blocking warning message.
+ .PP
+ \fBvsearch\fR operations are case insensitive, except when soft masking is
+-activated. For --usearch_global (searching), --cluster_fast and
+---cluster_smallmem (clustering), and --maskfasta (masking) commands,
++activated. For \-\-usearch_global (searching), \-\-cluster_fast and
++\-\-cluster_smallmem (clustering), and \-\-maskfasta (masking) commands,
+ the case is important if soft masking is used. Soft masking is
+-specified with the options "--dbmask soft" (for searching) or "--qmask
++specified with the options "\-\-dbmask soft" (for searching) or "\-\-qmask
+ soft" (for searching, clustering and masking). When using soft
+ masking, lower case letters indicate masked symbols, while upper case
+ letters indicate regular symbols. Masked symbols are never included in
+@@ -121,7 +121,7 @@ in result files.
+ When comparing sequences during chimera detection, dereplication,
+ searching and clustering, T and U are considered identical, regardless
+ of their case. If two symbols are non-identical, their alignment will
+-result in the negative mismatch score (default -4), except if one or
++result in the negative mismatch score (default \-4), except if one or
+ both of the symbols are ambiguous (RYSWKMDBHVN) in which case the
+ score is zero. Alignment of two identical ambiguous symbols (e.g. R vs
+ R) also receives a score of zero.
+@@ -138,27 +138,27 @@ searching). We start with general option
+ General options:
+ .RS
+ .TP 9
+-.B --help
++.B \-\-help
+ Display a short help and exit.
+ .TP
+-.B --version
++.B \-\-version
+ Output version information and exit.
+ .TP
+-.BI --fasta_width\~ "positive integer"
++.BI \-\-fasta_width\~ "positive integer"
+ Fasta files produced by \fBvsearch\fR are wrapped (sequences are
+ written on lines of \fIinteger\fR nucleotides, 80 by default). Set
+ that value to 0 to eliminate the wrapping.
+ .TP
+-.BI --maxseqlength\~ "positive integer"
++.BI \-\-maxseqlength\~ "positive integer"
+ All \fBvsearch\fR operations will discard sequences of length equal or
+ greater than \fIinteger\fR (50,000 nucleotides by default).
+ .TP
+-.BI --minseqlength\~ "positive integer"
++.BI \-\-minseqlength\~ "positive integer"
+ All \fBvsearch\fR operations will discard sequences of length smaller
+ than \fIinteger\fR (1 nucleotide by default for sorting or shuffling,
+ 32 nucleotides for clustering, dereplication or searching).
+ .TP
+-.B --notrunclabels
++.B \-\-notrunclabels
+ Do not truncate sequence labels at first space, use the full header in
+ output files.
+ .RE
+@@ -168,7 +168,7 @@ Chimera detection options:
+ .PP
+ .RS
+ Chimera detection is based on a scoring function controlled by five
+-options (--dn, --mindiffs, --mindiv, --minh, --xn). Sequences are first
++options (\-\-dn, \-\-mindiffs, \-\-mindiv, \-\-minh, \-\-xn). Sequences are first
+ sorted by decreasing abundance (if available), and compared on their
+ \fIplus\fR strand only (case insensitive).
+ .PP
+@@ -176,12 +176,12 @@ In \fIde novo\fR mode, input fasta file
+ annotations (pattern [;]size=\fIinteger\fR[;] in the fasta
+ header). The input order influences the chimera detection, we
+ recommend to sort sequences by decreasing abundance (default of
+---derep_fulllength command). If your sequence set needs to be sorted,
+-please see the --sortbysize command in the sorting section.
++\-\-derep_fulllength command). If your sequence set needs to be sorted,
++please see the \-\-sortbysize command in the sorting section.
+ .PP
+ .TP 9
+-.BI --abskew \0real
+-When using --uchime_denovo, the abundance skew is used to distinguish
++.BI \-\-abskew \0real
++When using \-\-uchime_denovo, the abundance skew is used to distinguish
+ in a 3-way alignment which sequence is the chimera and which are the
+ parents. The assumption is that chimeras appeared later in the PCR
+ amplification process and are therefore less abundant than their
+@@ -189,75 +189,75 @@ parents. The default value is 2.0, which
+ be at least 2 times more abundant than their chimera. Any positive
+ value greater than 1.0 can be used.
+ .TP
+-.BI --alignwidth\~ "positive integer"
+-Width of 3-way alignments in --uchimealns output. The default value is
++.BI \-\-alignwidth\~ "positive integer"
++Width of 3-way alignments in \-\-uchimealns output. The default value is
+ 80. Set to 0 to eliminate wrapping.
+ .TP
+-.BI --chimeras \0filename
++.BI \-\-chimeras \0filename
+ Output chimeric sequences to \fIfilename\fR, in fasta format. Output
+ order may vary when using multiple threads.
+ .TP
+-.BI --db \0filename
+-When using --uchime_ref, detect chimeras using the fasta-formatted
++.BI \-\-db \0filename
++When using \-\-uchime_ref, detect chimeras using the fasta-formatted
+ reference sequences contained in \fIfilename\fR. Reference sequences
+ are assumed to be chimera-free. Chimeras will not be detected if their
+ parents (or sufficiently close relatives) are not present in the
+ database.
+ .TP
+-.BI --dn \0real
++.BI \-\-dn \0real
+ No vote pseudo-count (parameter \fIn\fR in the chimera scoring
+ function) (1.4).
+ .TP
+-.BI --mindiffs\~ "positive integer"
++.BI \-\-mindiffs\~ "positive integer"
+ Minimum number of differences per segment (3).
+ .TP
+-.BI --mindiv \0real
++.BI \-\-mindiv \0real
+ Minimum divergence from closest parent (0.8).
+ .TP
+-.BI --minh \0real
++.BI \-\-minh \0real
+ Minimum score (h). Increasing this value tends to reduce the number of
+ false positives and to decrease sensitivity. Default value is
+ 0.28. (value ranging from 0.0 to 1.0 included).
+ .TP
+-.BI --nonchimeras \0filename
++.BI \-\-nonchimeras \0filename
+ Output non-chimeric sequences to \fIfilename\fR, in fasta
+ format. Output order may vary when using multiple threads.
+ .TP
+-.B --self
+-When using --uchime_ref, ignore a reference sequence when its label
++.B \-\-self
++When using \-\-uchime_ref, ignore a reference sequence when its label
+ matches the label of the query sequence (useful to estimate
+ false-positive rate in reference sequences).
+ .TP
+-.B --selfid
+-When using --uchime_ref, ignore a reference sequence when its
++.B \-\-selfid
++When using \-\-uchime_ref, ignore a reference sequence when its
+ nucleotide sequence is strictly identical with the query sequence.
+ .TP
+-.BI --threads\~ "positive integer"
++.BI \-\-threads\~ "positive integer"
+ Number of computation threads to use (1 to 256) with uchime_ref.
+ The number of threads
+ should be lesser or equal to the number of available CPU cores. The
+ default is to launch one thread per available logical core.
+ .TP
+-.BI --uchime_denovo \0filename
++.BI \-\-uchime_denovo \0filename
+ Detect chimeras present in the fasta-formatted \fIfilename\fR, without
+ external references (i.e. \fIde novo\fR). Automatically sort the
+ sequences in \fIfilename\fR by decreasing abundance
+ beforehand. Multithreading is not supported.
+ .TP
+-.BI --uchime_ref \0filename
++.BI \-\-uchime_ref \0filename
+ Detect chimeras present in the fasta-formatted \fIfilename\fR by
+-comparing them with reference sequences (option --db). Multithreading
++comparing them with reference sequences (option \-\-db). Multithreading
+ is supported.
+ .TP
+-.BI --uchimealns \0filename
++.BI \-\-uchimealns \0filename
+ Write 3-way global alignments (parentA, parentB, chimera) to
+-\fIfilename\fR using a human-readable format. Use --alignwidth to modify
++\fIfilename\fR using a human-readable format. Use \-\-alignwidth to modify
+ alignment length. Output order may vary when using multiple threads.
+ .TP
+-.BI --uchimeout \0filename
++.BI \-\-uchimeout \0filename
+ Write chimera detection results to \fIfilename\fR using the uchime
+ tab-separated format of 18 fields (see the list below). Use
+---uchimeout5 to use a format compatible with usearch v5 and earlier
++\-\-uchimeout5 to use a format compatible with usearch v5 and earlier
+ versions. Rows output order may vary when using multiple threads.
+ .RS
+ .RS
+@@ -272,7 +272,7 @@ A: parent A sequence label.
+ B: parent B sequence label.
+ .IP \n+[step].
+ T: top parent sequence label (i.e. parent most similar to the
+-query). That field is removed when using --uchimeout5.
++query). That field is removed when using \-\-uchimeout5.
+ .IP \n+[step].
+ idQM: percentage of similarity of query (Q) and model (M)
+ constructed as a part of parent A and a part of parent B.
+@@ -304,12 +304,12 @@ YN: query is chimeric (Y), or not (N), o
+ .RE
+ .RE
+ .TP
+-.B --uchimeout5
+-When using --uchimeout, write chimera detection results using a
+-tab-separated format of 17 fields (drop the 5th field of --uchimeout),
++.B \-\-uchimeout5
++When using \-\-uchimeout, write chimera detection results using a
++tab-separated format of 17 fields (drop the 5th field of \-\-uchimeout),
+ compatible with usearch version 5 and earlier versions.
+ .TP
+-.BI --xn \0real
++.BI \-\-xn \0real
+ No vote weight (parameter beta) (8.0).
+ .RE
+ .PP
+@@ -320,53 +320,53 @@ Clustering options:
+ \fBvsearch\fR implements a single-pass, greedy star-clustering
+ algorithm, similar to the algorithms implemented in usearch, DNAclust
+ and sumaclust. Important parameters are the global clustering
+-threshold (--id) and the pairwise identity definition (--iddef).
++threshold (\-\-id) and the pairwise identity definition (\-\-iddef).
+ .TP 9
+-.BI --centroids \0filename
++.BI \-\-centroids \0filename
+ Output cluster centroid sequences to \fIfilename\fR file, in fasta
+ format. The centroid is the sequence that seeded the cluster (i.e. the
+ first sequence of the cluster).
+ .TP
+-.BI --cluster_fast \0filename
++.BI \-\-cluster_fast \0filename
+ Clusterize the fasta sequences in \fIfilename\fR, automatically
+ perform a sorting by decreasing sequence length beforehand.
+ .TP
+-.BI --cluster_size \0filename
++.BI \-\-cluster_size \0filename
+ Clusterize the fasta sequences in \fIfilename\fR, automatically
+ perform a sorting by decreasing sequence abundance beforehand.
+ .TP
+-.BI --cluster_smallmem \0filename
++.BI \-\-cluster_smallmem \0filename
+ Clusterize the fasta sequences in \fIfilename\fR without automatically
+ modifying their order beforehand. Sequence are expected to be sorted
+-by decreasing sequence length, unless --usersort is used.
++by decreasing sequence length, unless \-\-usersort is used.
+ .TP
+-.BI --clusters \0string
++.BI \-\-clusters \0string
+ Output each cluster to a separate fasta file using the prefix
+ \fIstring\fR and a ticker (0, 1, 2, etc.) to construct the path and filenames.
+ .TP
+-.BI --consout \0filename
++.BI \-\-consout \0filename
+ Output cluster consensus sequences to \fIfilename\fR. For each
+ cluster, a multiple alignment is computed, and a consensus sequence is
+ constructed by taking the majority symbol (nucleotide or gap) from
+ each column of the alignment. Columns containing a majority of gaps
+-are skipped, except for terminal gaps. Use --construncate to take
++are skipped, except for terminal gaps. Use \-\-construncate to take
+ terminal gaps into account (not implemented yet).
+ .\" .TP
+-.\" .B --construncate
+-.\" when using the --consout option to build consensus sequences, do not
++.\" .B \-\-construncate
++.\" when using the \-\-consout option to build consensus sequences, do not
+ .\" ignore terminal gaps. That option skips terminal columns if they
+ .\" contain a majority of gaps, yielding shorter consensus sequences than
+-.\" when using --consout alone.
++.\" when using \-\-consout alone.
+ .TP
+-.BI --id \0real
++.BI \-\-id \0real
+ Do not add the target to the cluster if the pairwise identity with the
+ centroid is lower than \fIreal\fR (value ranging from 0.0 to 1.0
+ included). The pairwise identity is defined as the number of (matching
+ columns) / (alignment length - terminal gaps). That definition can be
+-modified by --iddef.
++modified by \-\-iddef.
+ .TP
+-.BI --iddef\~ "0|1|2|3|4"
+-Change the pairwise identity definition used in --id. Values accepted
++.BI \-\-iddef\~ "0|1|2|3|4"
++Change the pairwise identity definition used in \-\-id. Values accepted
+ are:
+ .RS
+ .RS
+@@ -381,68 +381,68 @@ edit distance excluding terminal gaps (d
+ Marine Biological Lab definition counting each extended gap as a
+ single difference.
+ .IP \n+[step].
+-BLAST definition, equivalent to --iddef 2 in a context of global
++BLAST definition, equivalent to \-\-iddef 2 in a context of global
+ pairwise alignment.
+ .RE
+ .RE
+ .TP
+-.BI --msaout \0filename
++.BI \-\-msaout \0filename
+ Output a multiple sequence alignment and a consensus sequence for each
+ cluster to \fIfilename\fR, in fasta format. The consensus sequence is
+ constructed by taking the majority symbol (nucleotide or gap) from
+ each column of the alignment. Columns containing a majority of gaps
+ are skipped, except for terminal gaps.
+ .TP
+-.BI --qmask\~ "none|dust|soft"
++.BI \-\-qmask\~ "none|dust|soft"
+ Mask simple repeats and low-complexity regions in sequences using the
+ \fIdust\fR or the \fIsoft\fR algorithms, or do not mask
+ (\fInone\fR). Warning, when using \fIsoft\fR masking, clustering
+ becomes case sensitive. The default is to mask using \fIdust\fR.
+ .TP
+-.B --sizein
++.B \-\-sizein
+ Take into account the abundance annotations present in the input fasta
+ file (search for the pattern "[>;]size=\fIinteger\fR[;]" in sequence
+ headers).
+ .TP
+-.B --sizeout
++.B \-\-sizeout
+ Add abundance annotations to the output fasta files (add the pattern
+-";size=\fIinteger\fR;" to sequence headers). If --sizein is specified,
++";size=\fIinteger\fR;" to sequence headers). If \-\-sizein is specified,
+ abundance annotations are reported to output files, and each cluster
+ centroid receives a new abundance value corresponding to the total
+-abundance of the amplicons included in the cluster (--centroids
+-option). If --sizein is not specified, input abundances are set to 1
++abundance of the amplicons included in the cluster (\-\-centroids
++option). If \-\-sizein is not specified, input abundances are set to 1
+ for amplicons, and to the number of amplicons per cluster for
+ centroids.
+ .TP
+-.BI --strand\~ "plus|both"
++.BI \-\-strand\~ "plus|both"
+ When comparing sequences with the cluster seed, check the \fIplus\fR
+ strand only (default) or check \fIboth\fR strands.
+ .TP
+-.BI --threads\~ "positive integer"
++.BI \-\-threads\~ "positive integer"
+ Number of computation threads to use (1 to 256). The number of threads
+ should be less or equal to the number of available CPU cores. The
+ default is to launch one thread per available logical core.
+ .TP
+-.BI --uc \0filename
++.BI \-\-uc \0filename
+ Output clustering results in \fIfilename\fR using a uclust-like
+ format. See <http://www.drive5.com/usearch/manual/ucout.html> for a
+ description of the format.
+ .TP
+-.B --usersort
+-When using --cluster_smallmem, allow any sequence input order, not
++.B \-\-usersort
++When using \-\-cluster_smallmem, allow any sequence input order, not
+ just a decreasing length ordering.
+ .TP
+ Most searching options also apply to clustering:
+ .br
+---alnout, --blast6out, --userout, --userfields, --fastapairs, --matched,
+---notmatched, --maxaccept, --maxreject, score filtering, gap penalties, masking. (see the Searching section).
++\-\-alnout, \-\-blast6out, \-\-userout, \-\-userfields, \-\-fastapairs, \-\-matched,
++\-\-notmatched, \-\-maxaccept, \-\-maxreject, score filtering, gap penalties, masking. (see the Searching section).
+ .RE
+ .PP
+ .\" ----------------------------------------------------------------------------
+ Dereplication options:
+ .RS
+ .TP 9
+-.BI --derep_fulllength \0filename
++.BI \-\-derep_fulllength \0filename
+ Merge strictly identical sequences contained in
+ \fIfilename\fR. Identical sequences are defined as having the same
+ length and the same string of nucleotides (case insensitive, T and U
+@@ -450,46 +450,46 @@ are considered the same). As \fBvsearch\
+ \fIfilename\fR twice, \fIfilename\fR must be a real file, not a
+ stream.
+ .TP
+-.BI --maxuniquesize\~ "positive integer"
++.BI \-\-maxuniquesize\~ "positive integer"
+ Discard sequences with an abundance value greater than \fIinteger\fR.
+ .TP
+ .BI --minuniquesize\~ "positive integer"
+ Discard sequences with an abundance value smaller than \fIinteger\fR.
+ .TP
+-.BI --output \0filename
++.BI \-\-output \0filename
+ Write the dereplicated sequences to \fIfilename\fR, in fasta format
+ and sorted by decreasing abundance. Identical sequences receive the
+-header of the first sequence of their group. If --sizeout is used, the
++header of the first sequence of their group. If \-\-sizeout is used, the
+ number of occurrences (i.e. abundance) of each sequence is indicated
+ at the end of their fasta header using the pattern
+ ";size=\fIinteger\fR;".
+ .TP
+-.B --sizein
++.B \-\-sizein
+ Take into account the abundance annotations present in the input fasta
+ file (search for the pattern "[>;]size=\fIinteger\fR[;]" in sequence
+ headers).
+ .TP
+-.B --sizeout
++.B \-\-sizeout
+ Add abundance annotations to the output fasta file (add the pattern
+-";size=\fIinteger\fR;" to sequence headers).  If --sizein is specified,
++";size=\fIinteger\fR;" to sequence headers).  If \-\-sizein is specified,
+ each unique sequence receives a new abundance value corresponding to
+ its total abundance (sum of the abundances of its occurrences). If
+---sizein is not specified, input abundances are set to 1, and each
++\-\-sizein is not specified, input abundances are set to 1, and each
+ unique sequence receives a new abundance value corresponding to its
+ number of occurrences in the input file.
+ .TP
+-.BI --strand\~ "plus|both"
++.BI \-\-strand\~ "plus|both"
+ When searching for strictly identical sequences, check the \fIplus\fR
+ strand only (default) or check \fIboth\fR strands.
+ .TP
+-.BI --topn\~ "positive integer"
++.BI \-\-topn\~ "positive integer"
+ Output only the top \fIinteger\fR sequences (i.e. the most abundant).
+ .TP
+-.BI --uc \0filename
++.BI \-\-uc \0filename
+ Output dereplication results in \fIfilename\fR using a uclust-like
+ format. See <http://www.drive5.com/usearch/manual/ucout.html> for a
+ description of the format. In the context of dereplication, the option
+---uc_allhits has no effect.
++\-\-uc_allhits has no effect.
+ .RE
+ .PP
+ .\" ----------------------------------------------------------------------------
+@@ -498,9 +498,9 @@ Masking options:
+ .PP
+ An input sequence can be composed of lower- or uppercase
+ nucleotides. Lowercase nucleotides are silently set to uppercase
+-before masking, unless the --qmask soft option is used. Here are the
+-results of combined masking options --qmask (or --dbmask for database
+-sequences) and --hardmask, assuming each input sequences contains both
++before masking, unless the \-\-qmask soft option is used. Here are the
++results of combined masking options \-\-qmask (or \-\-dbmask for database
++sequences) and \-\-hardmask, assuming each input sequences contains both
+ lower and uppercase nucleotides:
+ .PP
+ .TS
+@@ -518,24 +518,24 @@ soft:on:lowercase symbols masked and cha
+ .TE
+ .PP
+ .TP 9
+-.B --hardmask
++.B \-\-hardmask
+ Mask low-complexity regions by replacing them with Ns instead of
+ setting them to lower case.
+ .TP
+-.BI --maskfasta \0filename
++.BI \-\-maskfasta \0filename
+ Mask simple repeats and low-complexity regions in sequences contained
+ in \fIfilename\fR. The default is to mask using \fIdust\fR (use
+---qmask to modify that behavior).
++\-\-qmask to modify that behavior).
+ .TP
+-.BI --output \0filename
++.BI \-\-output \0filename
+ Write the masked sequences to \fIfilename\fR, in fasta format.
+ .TP
+-.BI --qmask\~ "none|dust|soft"
++.BI \-\-qmask\~ "none|dust|soft"
+ Mask simple repeats and low-complexity regions in sequences using the
+ \fIdust\fR or the \fIsoft\fR algorithms, or do not mask
+ (\fInone\fR). The default is to mask using \fIdust\fR.
+ .TP
+-.BI --threads\~ "positive integer"
++.BI \-\-threads\~ "positive integer"
+ Number of computation threads to use (1 to 256). The number of threads
+ should be lesser or equal to the number of available CPU cores. The
+ default is to launch one thread per available logical core.
+@@ -545,26 +545,26 @@ default is to launch one thread per avai
+ Pairwise alignment options:
+ .RS
+ .TP 9
+-.BI --allpairs_global \0filename
++.BI \-\-allpairs_global \0filename
+ Perform optimal global pairwise alignments of all vs. all fasta
+ sequences contained in \fIfilename\fR. The results of the n * (n-1) /
+-2 alignments are written to the result files specified with --alnout,
+---blast6out, --fastapairs --matched, --notmatched, --uc or --userout
+-(see Searching section below). Specify either the --acceptall option
++2 alignments are written to the result files specified with \-\-alnout,
++\-\-blast6out, \-\-fastapairs \-\-matched, \-\-notmatched, \-\-uc or \-\-userout
++(see Searching section below). Specify either the \-\-acceptall option
+ to output all pairwise alignments, or specify an identity level with
+---id to discard weak alignments. Most other accept/reject options (see
++\-\-id to discard weak alignments. Most other accept/reject options (see
+ Searching options below) may also be used. Sequences are aligned on
+ their \fIplus\fR strand only. This command is multi-threaded.
+ .TP
+-.B --acceptall
++.B \-\-acceptall
+ Write the results of all alignments to output files. This option
+-overrides all other accept/reject options (e.g. --id).
++overrides all other accept/reject options (e.g. \-\-id).
+ .TP
+-.BI --id \0real
++.BI \-\-id \0real
+ Reject the sequence match if the pairwise identity is lower than
+ \fIreal\fR (value ranging from 0.0 to 1.0 included).
+ .TP
+-.BI --threads\~ "positive integer"
++.BI \-\-threads\~ "positive integer"
+ Number of computation threads to use (1 to 256). The number of threads
+ should be lesser or equal to the number of available CPU cores. The
+ default is to launch one thread per available logical core.
+@@ -574,17 +574,17 @@ default is to launch one thread per avai
+ Searching options:
+ .RS
+ .TP 9
+-.BI --alnout \0filename
++.BI \-\-alnout \0filename
+ Write pairwise global alignments to \fIfilename\fR using a
+-human-readable format. Use --rowlen to modify alignment length. Output
++human-readable format. Use \-\-rowlen to modify alignment length. Output
+ order may vary when using multiple threads.
+ .TP
+-.BI --blast6out \0filename
++.BI \-\-blast6out \0filename
+ Write search results to \fIfilename\fR using a blast-like
+ tab-separated format of twelve fields (listed below), with one line
+-per query-target matching (or lack of matching if --output_no_hits is
++per query-target matching (or lack of matching if \-\-output_no_hits is
+ used). Output order may vary when using multiple threads. A similar
+-output can be obtain with --userout \fIfilename\fR and --userfields
++output can be obtain with \-\-userout \fIfilename\fR and \-\-userfields
+ query+target+id+alnlen+mism+opens+qlo+qhi+tlo+thi+evalue+bits.
+ A complete list and description is available in the section "Userfields"
+ of this manual.
+@@ -628,52 +628,52 @@ query. Nucleotide numbering starts from
+ there is no alignment.
+ .IP \n+[step].
+ \fIevalue\fR: expectancy-value (not computed for nucleotide
+-alignments). Always set to -1.
++alignments). Always set to \-1.
+ .IP \n+[step].
+ \fIbits\fR: bit score (not computed for nucleotide
+ alignments). Always set to 0.
+ .RE
+ .RE
+ .TP
+-.BI --db \0filename
+-Compare query sequences (specified with --usearch_global)
++.BI \-\-db \0filename
++Compare query sequences (specified with \-\-usearch_global)
+ to the fasta-formatted target sequences contained in \fIfilename\fR,
+ using global pairwise alignment.
+ .TP
+-.BI --dbmask\~ "none|dust|soft"
++.BI \-\-dbmask\~ "none|dust|soft"
+ Mask simple repeats and low-complexity regions in target database
+ sequences using the \fIdust\fR or the \fIsoft\fR algorithms, or do not
+ mask (\fInone\fR). Warning, when using \fIsoft\fR masking search
+ commands become case sensitive. The default is to mask using
+ \fIdust\fR.
+ .TP
+-.BI --dbmatched \0filename
++.BI \-\-dbmatched \0filename
+ Write database target sequences matching at least one query sequence
+-to \fIfilename\fR, in fasta format. If the option --sizeout is used,
++to \fIfilename\fR, in fasta format. If the option \-\-sizeout is used,
+ the number of queries that matched each target sequence is indicated
+ using the pattern ";size=\fIinteger\fR;".
+ .TP
+-.BI --dbnotmatched \0filename
++.BI \-\-dbnotmatched \0filename
+ Write database target sequences not matching query sequences to
+ \fIfilename\fR, in fasta format.
+ .TP
+-.BI --fastapairs \0filename
++.BI \-\-fastapairs \0filename
+ Write pairwise alignments of query and target sequences to
+ \fIfilename\fR, in fasta format.
+ .TP
+-.B --fulldp
++.B \-\-fulldp
+ Dummy option. To maximize search sensitivity, \fBvsearch\fR uses a
+ 8-way 16-bit SIMD vectorized full dynamic programming algorithm
+-(Needleman-Wunsch), whether or not --fulldp is specified.
++(Needleman-Wunsch), whether or not \-\-fulldp is specified.
+ .TP
+-.BI --gapext \0string
+-Set penalties for a gap extension. See --gapopen for a complete
++.BI \-\-gapext \0string
++Set penalties for a gap extension. See \-\-gapopen for a complete
+ description of the penalty declaration system. The default is to
+ initialize the six gap extending penalties using a penalty of 2 for
+ extending internal gaps and a penalty of 1 for extending terminal
+ gaps, in both query and target sequences (i.e. 2I/1E).
+ .TP
+-.BI --gapopen \0string
++.BI \-\-gapopen \0string
+ Set penalties for a gap opening. A gap opening can occur in six
+ different contexts: in the query (Q) or in the target (T) sequence, at
+ the left (L) or right (R) extremity of the sequence, or inside the
+@@ -704,12 +704,12 @@ gap penalties. Because the lowest gap pe
+ in usearch, all default scores and gap penalties in \fBvsearch\fR
+ have been doubled in order to obtain similar alignments.
+ .TP
+-.B --hardmask
++.B \-\-hardmask
+ Mask low-complexity regions by replacing them with Ns instead of
+ setting them to lower case. For more information, please see the
+ Masking section.
+ .TP
+-.BI --id \0real
++.BI \-\-id \0real
+ Reject the sequence match if the pairwise identity is lower than
+ \fIreal\fR (value ranging from 0.0 to 1.0 included). The search
+ process sorts target sequences by decreasing number of \fIk\fR-mers
+@@ -719,13 +719,13 @@ also prevent pairwise alignments with we
+ there needs to be at least 6 shared \fIk\fR-mers to start the pairwise
+ alignment, and at least one out of every 16 \fIk\fR-mers from the
+ query needs to match the target. Consequently, using values lower than
+---id 0.5 is not likely to capture more weakly matching targets. The
++\-\-id 0.5 is not likely to capture more weakly matching targets. The
+ pairwise identity is by default defined as the number of (matching columns) /
+ (alignment length - terminal gaps). That definition can be modified by
+---iddef.
++\-\-iddef.
+ .TP
+-.BI --iddef\~ "0|1|2|3|4"
+-Change the pairwise identity definition used in --id. Values accepted
++.BI \-\-iddef\~ "0|1|2|3|4"
++Change the pairwise identity definition used in \-\-id. Values accepted
+ are:
+ .RS
+ .RS
+@@ -735,40 +735,40 @@ CD-HIT definition using shortest sequenc
+ .IP \n+[step].
+ edit distance.
+ .IP \n+[step].
+-edit distance excluding terminal gaps (default value of --id).
++edit distance excluding terminal gaps (default value of \-\-id).
+ .IP \n+[step].
+ Marine Biological Lab definition counting each extended gap as a
+ single difference.
+ .IP \n+[step].
+-BLAST definition, equivalent to --iddef 2 in a context of global
++BLAST definition, equivalent to \-\-iddef 2 in a context of global
+ pairwise alignment.
+ .RE
+ .RE
+ .PP
+-The option --userfields accepts the fields id0 to id4, in addition to
++The option \-\-userfields accepts the fields id0 to id4, in addition to
+ the field id, to report the pairwise identity values corresponding to
+ the different definitions.
+ .TP
+-.BI --idprefix\~ "positive integer"
++.BI \-\-idprefix\~ "positive integer"
+ Reject the target sequence if the first \fIinteger\fR nucleotides do
+ not match the query sequence.
+ .TP
+-.BI --idsuffix\~ "positive integer"
++.BI \-\-idsuffix\~ "positive integer"
+ Reject the target sequence if the last \fIinteger\fR nucleotides do
+ not match the query sequence.
+ .TP
+-.B --leftjust
++.B \-\-leftjust
+ Reject the target sequence if the alignment begins with gaps.
+ .TP
+-.BI --match\~ "integer"
++.BI \-\-match\~ "integer"
+ Score assigned to a match (i.e. identical nucleotides) in the pairwise
+ alignment. The default value is 2.
+ .TP
+-.BI --matched \0filename
++.BI \-\-matched \0filename
+ Write query sequences matching database target sequences to
+ \fIfilename\fR, in fasta format.
+ .TP
+-.BI --maxaccepts\~ "positive integer"
++.BI \-\-maxaccepts\~ "positive integer"
+ Maximum number of hits to accept before stopping the search. The
+ default value is 1. This option works in pair with maxrejects. The
+ search process sorts target sequences by decreasing number of
+@@ -779,31 +779,31 @@ and the search process stops for that qu
+ higher value, more hits are accepted. If maxaccepts and maxrejects are
+ both set to 0, the complete database is searched.
+ .TP
+-.BI --maxdiffs\~ "positive integer"
++.BI \-\-maxdiffs\~ "positive integer"
+ Reject the target sequence if the alignment contains at least
+ \fIinteger\fR substitutions, insertions or deletions.
+ .TP
+-.BI --maxgaps\~ "positive integer"
++.BI \-\-maxgaps\~ "positive integer"
+ Reject the target sequence if the alignment contains at least
+ \fIinteger\fR insertions or deletions.
+ .TP
+-.BI --maxhits\~ "positive integer"
++.BI \-\-maxhits\~ "positive integer"
+ Maximum number of hits to show once the search is terminated (hits are
+ sorted by decreasing identity). Unlimited by default value. \fBIt
+ applies to alnout, blast6out, uc, userout, fastapairs\fR.
+ .TP
+-.BI --maxid \0real
++.BI \-\-maxid \0real
+ Reject the target sequence if its percentage of identity with the
+ query is greater than \fIreal\fR.
+ .TP
+-.BI --maxqsize\~ "positive integer"
++.BI \-\-maxqsize\~ "positive integer"
+ Reject query sequences with an abundance greater than
+ \fIinteger\fR.
+ .TP
+-.BI --maxqt \0real
++.BI \-\-maxqt \0real
+ Reject if the query/target sequence length ratio is greater than \fIreal\fR.
+ .TP
+-.BI --maxrejects\~ "positive integer"
++.BI \-\-maxrejects\~ "positive integer"
+ Maximum number of non-matching target sequences to consider before
+ stopping the search. The default value is 32. This option works in
+ pair with maxaccepts. The search process sorts target sequences by
+@@ -815,138 +815,138 @@ hit). If maxrejects is set to a higher v
+ are considered. If maxaccepts and maxrejects are both set to 0, the
+ complete database is searched.
+ .TP
+-.BI --maxsizeratio \0real
++.BI \-\-maxsizeratio \0real
+ Reject if the query/target abundance ratio is greater than
+ \fIreal\fR.
+ .TP
+-.BI --maxsl \0real
++.BI \-\-maxsl \0real
+ Reject if the shorter/longer sequence length ratio is
+ greater than \fIreal\fR.
+ .TP
+-.BI --maxsubs\~ "positive integer"
++.BI \-\-maxsubs\~ "positive integer"
+ Reject the target sequence if the alignment contains more than
+ \fIinteger\fR substitutions.
+ .TP
+-.BI --mid \0real
++.BI \-\-mid \0real
+ Reject the alignment if the percentage of identity is lower than
+ \fIreal\fR (ignoring all gaps, internal and terminal).
+ .TP
+-.BI --mincols\~ "positive integer"
++.BI \-\-mincols\~ "positive integer"
+ Reject the target sequence if the alignment length is shorter than
+ \fIinteger\fR.
+ .TP
+-.BI --minqt \0real
++.BI \-\-minqt \0real
+ Reject if the query/target sequence length ratio is lower than
+ \fIreal\fR.
+ .TP
+-.BI --minsizeratio \0real
++.BI \-\-minsizeratio \0real
+ Reject if the query/target abundance ratio is lower than \fIreal\fR.
+ .TP
+-.BI --minsl \0real
++.BI \-\-minsl \0real
+ Reject if the shorter/longer sequence length ratio is lower than
+ \fIreal\fR.
+ .TP
+-.BI --mintsize\~ "positive integer"
++.BI \-\-mintsize\~ "positive integer"
+ Reject target sequences with an abundance lower than \fIinteger\fR.
+ .TP
+-.BI --mismatch\~ "integer"
++.BI \-\-mismatch\~ "integer"
+ Score assigned to a mismatch (i.e. different nucleotides) in the
+-pairwise alignment. The default value is -4.
++pairwise alignment. The default value is \-4.
+ .TP
+-.BI --notmatched \0filename
++.BI \-\-notmatched \0filename
+ Write query sequences not matching database target sequences to
+ \fIfilename\fR, in fasta format.
+ .TP
+-.B --output_no_hits
+-Write both matching and non-matching queries to --alnout, --blast6out,
+-and --userout output files (--uc and --uc_allhits output files always
++.B \-\-output_no_hits
++Write both matching and non-matching queries to \-\-alnout, \-\-blast6out,
++and \-\-userout output files (\-\-uc and \-\-uc_allhits output files always
+ feature non-matching queries). Non-matching queries are labelled "No
+-hits" in --alnout files.
++hits" in \-\-alnout files.
+ .TP
+-.BI --qmask\~ "none|dust|soft"
++.BI \-\-qmask\~ "none|dust|soft"
+ Mask simple repeats and low-complexity regions in query sequences
+ using the \fIdust\fR or the \fIsoft\fR algorithms, or do not mask
+ (\fInone\fR). Warning, when using \fIsoft\fR masking search commands
+ become case sensitive. The default is to mask using \fIdust\fR.
+ .TP
+-.BI --query_cov \0real
++.BI \-\-query_cov \0real
+ Reject if the fraction of the query aligned to the target sequence is
+ lower than \fIreal\fR. The query coverage is computed as
+ (matches + mismatches) / query sequence length. Internal or terminal
+ gaps are not taken into account.
+ .TP
+-.B --rightjust
++.B \-\-rightjust
+ Reject the target sequence if the alignment ends with gaps.
+ .TP
+-.BI --rowlen\~ "positive integer"
+-Width of alignment lines in --alnout output. The default value is
++.BI \-\-rowlen\~ "positive integer"
++Width of alignment lines in \-\-alnout output. The default value is
+ 64. Set to 0 to eliminate wrapping.
+ .TP
+-.B --self
++.B \-\-self
+ Reject the alignment if the query and target labels are identical.
+ .TP
+-.B --selfid
++.B \-\-selfid
+ Reject the alignment if the query and target sequences are strictly
+ identical.
+ .TP
+-.B --sizeout
+-Add abundance annotations to the output of the option --dbmatched
++.B \-\-sizeout
++Add abundance annotations to the output of the option \-\-dbmatched
+ (using the pattern ";size=\fIinteger\fR;").
+ .TP
+-.BI --strand\~ "plus|both"
++.BI \-\-strand\~ "plus|both"
+ When searching for similar sequences, check the \fIplus\fR strand only
+ (default) or check \fIboth\fR strands.
+ .TP
+-.BI --target_cov \0real
++.BI \-\-target_cov \0real
+ Reject if the fraction of the target sequence aligned to the query
+ sequence is lower than \fIreal\fR. The target coverage is computed as
+ (matches + mismatches) / target sequence length.
+ Internal or terminal gaps are not taken into account.
+ .TP
+-.BI --threads\~ "positive integer"
++.BI \-\-threads\~ "positive integer"
+ Number of computation threads to use (1 to 256). The number of threads
+ should be lesser or equal to the number of available CPU cores. The
+ default is to launch one thread per available logical core.
+ .TP
+-.B --top_hits_only
++.B \-\-top_hits_only
+ Output only the hits with the highest percentage of identity with the
+ query.
+ .TP
+-.BI --uc \0filename
++.BI \-\-uc \0filename
+ Output searching results in \fIfilename\fR using a uclust-like
+ format. See <http://www.drive5.com/usearch/manual/ucout.html> for a
+ description of the format. Output order may vary when using multiple
+ threads.
+ .TP
+-.B --uc_allhits
+-When using the --uc option, show all hits, not just the top hit for
++.B \-\-uc_allhits
++When using the \-\-uc option, show all hits, not just the top hit for
+ each query.
+ .TP
+-.BI --usearch_global \0filename
+-Compare target sequences (--db) to the fasta-formatted query sequences
++.BI \-\-usearch_global \0filename
++Compare target sequences (\-\-db) to the fasta-formatted query sequences
+ contained in \fIfilename\fR, using global pairwise alignment.
+ .TP
+-.BI --userfields \0string
+-When using --userout, select and order the fields written to the
++.BI \-\-userfields \0string
++When using \-\-userout, select and order the fields written to the
+ output file. Fields are separated by "+" (e.g. query+target+id). See
+ the "Userfields" section for a complete list of fields.
+ .TP
+-.BI --userout \0filename
++.BI \-\-userout \0filename
+ Write user-defined tab-separated output to \fIfilename\fR. Select the
+-fields with the option --userfields. Output order may vary when using
+-multiple threads. If --userfields is empty or not present,
++fields with the option \-\-userfields. Output order may vary when using
++multiple threads. If \-\-userfields is empty or not present,
+ \fIfilename\fR is empty.
+ .TP
+-.BI --weak_id \0real
++.BI \-\-weak_id \0real
+ Show hits with percentage of identity of at least \fIreal\fR, without
+ terminating the search. A normal search stops as soon as enough hits
+-are found (as defined by --maxaccepts, --maxrejects, and --id). As
+---weak_id reports weak hits that are not deduced from --maxaccepts,
+-high --id values can be used, hence preserving both speed and
++are found (as defined by \-\-maxaccepts, \-\-maxrejects, and \-\-id). As
++\-\-weak_id reports weak hits that are not deduced from \-\-maxaccepts,
++high \-\-id values can be used, hence preserving both speed and
+ sensitivity. Logically, \fIreal\fR must be smaller than the value
+-indicated by --id.
++indicated by \-\-id.
+ .TP
+-.BI --wordlength\~ "positive integer"
++.BI \-\-wordlength\~ "positive integer"
+ Length of words (i.e. \fIk\fR-mers) for database indexing. The range
+ of possible values goes from 3 to 15, but values near 8 are generally
+ recommended. Longer words may reduce the sensitivity for weak
+@@ -963,75 +963,75 @@ more). The default value is 8.
+ Shuffling options:
+ .RS
+ .TP 9
+-.BI --output \0filename
++.BI \-\-output \0filename
+ Write the shuffled sequences to \fIfilename\fR, in fasta format.
+ .TP
+-.BI --seed\~ "positive integer"
++.BI \-\-seed\~ "positive integer"
+ When shuffling sequence order, use \fIinteger\fR as seed. A given seed
+ will always produce the same output order (useful for
+ replicability). Set to 0 to use a pseudo-random seed (default
+ behavior).
+ .TP
+-.BI --shuffle \0filename
++.BI \-\-shuffle \0filename
+ Pseudo-randomly shuffle the order of sequences contained in
+ \fIfilename\fR.
+ .TP
+-.BI --topn\~ "positive integer"
++.BI \-\-topn\~ "positive integer"
+ Output only the top \fIinteger\fR sequences.
+ .RE
+ .PP
+ .\" ----------------------------------------------------------------------------
+ Sorting options:
+ .RS
+-Fasta entries are sorted by decreasing abundance (--sortbysize) or
+-sequence length (--sortbylength). To obtain a stable sorting order,
++Fasta entries are sorted by decreasing abundance (\-\-sortbysize) or
++sequence length (\-\-sortbylength). To obtain a stable sorting order,
+ ties are sorted by decreasing abundance and label increasing
+-alpha-numerical order (--sortbylength), or just by label increasing
+-alpha-numerical order (--sortbysize). Label sorting assumes that all
++alpha-numerical order (\-\-sortbylength), or just by label increasing
++alpha-numerical order (\-\-sortbysize). Label sorting assumes that all
+ sequences have unique labels. The same applies to the automatic
+-sorting performed during chimera checking (--uchime_denovo),
+-dereplication (--derep_fulllength), and clustering (--cluster_fast and
+---cluster_size).
++sorting performed during chimera checking (\-\-uchime_denovo),
++dereplication (\-\-derep_fulllength), and clustering (\-\-cluster_fast and
++\-\-cluster_size).
+ .PP
+ .TP 9
+-.BI --maxsize\~ "positive integer"
+-When using --sortbysize, discard sequences with an abundance value
++.BI \-\-maxsize\~ "positive integer"
++When using \-\-sortbysize, discard sequences with an abundance value
+ greater than \fIinteger\fR.
+ .TP
+-.BI --minsize\~ "positive integer"
+-When using --sortbysize, discard sequences with an abundance value
++.BI \-\-minsize\~ "positive integer"
++When using \-\-sortbysize, discard sequences with an abundance value
+ smaller than \fIinteger\fR.
+ .TP
+-.BI --output \0filename
++.BI \-\-output \0filename
+ Write the sorted sequences to \fIfilename\fR, in fasta format.
+ .TP
+-.BI --relabel \0string
++.BI \-\-relabel \0string
+ Relabel sequence using the prefix \fIstring\fR and a ticker (1, 2, 3,
+-etc.) to construct the new headers. Use --sizeout to conserve the
++etc.) to construct the new headers. Use \-\-sizeout to conserve the
+ abundance annotations.
+ .TP
+-.B --sizeout
+-When using --relabel, report abundance annotations to the output fasta
++.B \-\-sizeout
++When using \-\-relabel, report abundance annotations to the output fasta
+ file (using the pattern ";size=\fIinteger\fR;").
+ .TP
+-.BI --sortbylength \0filename
++.BI \-\-sortbylength \0filename
+ Sort by decreasing length the sequences contained in
+-\fIfilename\fR. See the general options --minseqlength and
+---maxseqlength to eliminate short and long sequences.
++\fIfilename\fR. See the general options \-\-minseqlength and
++\-\-maxseqlength to eliminate short and long sequences.
+ .TP
+-.BI --sortbysize \0filename
++.BI \-\-sortbysize \0filename
+ Sort by decreasing abundance the sequences contained in \fIfilename\fR
+ (the pattern "[>;]size=\fIinteger\fR[;]" has to be present). See the
+-options --minsize and --maxsize to eliminate rare and dominant
++options \-\-minsize and \-\-maxsize to eliminate rare and dominant
+ sequences.
+ .TP
+-.BI --topn\~ "positive integer"
++.BI \-\-topn\~ "positive integer"
+ Output only the top \fIinteger\fR sequences (i.e. the longest or the
+ most abundant).
+ .RE
+ .PP
+ .\" ----------------------------------------------------------------------------
+-Userfields (fields accepted by the --userfields option):
++Userfields (fields accepted by the \-\-userfields option):
+ .RS
+ .TP 9
+ .B aln
+@@ -1052,7 +1052,7 @@ format (Compact Idiosyncratic Gapped Ali
+ (deletion) and I (insertion). Empty field if there is no alignment.
+ .TP
+ .B evalue
+-E-value (not computed for nucleotide alignments). Always set to -1.
++E-value (not computed for nucleotide alignments). Always set to \-1.
+ .TP
+ .B exts
+ Number of columns containing a gap extension (zero or positive integer
+@@ -1088,7 +1088,7 @@ single difference.
+ .TP
+ .B id4
+ BLAST definition of the percentage of identity (real value ranging
+-from 0.0 to 100.0), equivalent to --iddef 2 in a context of global
++from 0.0 to 100.0), equivalent to \-\-iddef 2 in a context of global
+ pairwise alignment.
+ .TP
+ .B ids
+@@ -1129,7 +1129,7 @@ Internal or terminal gaps are not taken
+ field is set to 0.0 if there is no alignment.
+ .TP
+ .B qframe
+-Query frame (-3 to +3). That field only concerns coding sequences and
++Query frame (\-3 to +3). That field only concerns coding sequences and
+ is not computed by \fBvsearch\fR. Always set to +0.
+ .TP
+ .B qhi
+@@ -1189,7 +1189,7 @@ Internal or terminal gaps are not taken
+ The field is set to 0.0 if there is no alignment.
+ .TP
+ .B tframe
+-Target frame (-3 to +3). That field only concerns coding sequences and
++Target frame (\-3 to +3). That field only concerns coding sequences and
+ is not computed by \fBvsearch\fR. Always set to +0.
+ .TP
+ .B thi
+@@ -1240,31 +1240,31 @@ quirks and inconsistencies. We decided n
+ and for complete transparency, to document here the deliberate changes
+ we made.
+ .PP
+-During a search with usearch, when using the options --blast6out and
+---output_no_hits, for queries with no match the number of fields
++During a search with usearch, when using the options \-\-blast6out and
++\-\-output_no_hits, for queries with no match the number of fields
+ reported is 13, where it should be 12. This is corrected in
+ \fBvsearch\fR.
+ .PP
+-The field raw of the --userfields option is not informative in
++The field raw of the \-\-userfields option is not informative in
+ usearch. This is corrected in \fBvsearch\fR.
+ .PP
+ The fields qlo, qhi, tlo, thi now have counterparts (qilo, qihi, tilo,
+ tihi) reporting alignment coordinates ignoring terminal gaps.
+ .PP
+-In usearch, when using the option --output_no_hits, queries that
++In usearch, when using the option \-\-output_no_hits, queries that
+ receive no match are reported in blast6out file, but not in the
+ alignment output file. This is corrected in \fBvsearch\fR.
+ .PP
+-\fBvsearch\fR introduces a new --cluster_size command that sorts
++\fBvsearch\fR introduces a new \-\-cluster_size command that sorts
+ sequences by decreasing abundance before clustering.
+ .PP
+-\fBvsearch\fR reintroduces --iddef alternative pairwise identity
++\fBvsearch\fR reintroduces \-\-iddef alternative pairwise identity
+ definitions that were removed from usearch.
+ .PP
+-\fBvsearch\fR extends the --topn option to sorting commands.
++\fBvsearch\fR extends the \-\-topn option to sorting commands.
+ .PP
+-\fBvsearch\fR extends the --sizein option to dereplication
+-(--derep_fulllength) and clustering (--cluster_fast).
++\fBvsearch\fR extends the \-\-sizein option to dereplication
++(\-\-derep_fulllength) and clustering (\-\-cluster_fast).
+ .PP
+ \fBvsearch\fR treats T and U as identical nucleotides for
+ dereplication.
+@@ -1296,8 +1296,8 @@ Cluster with a 97% similarity threshold,
+ and write cluster descriptions using a uclust-like format:
+ .PP
+ .RS
+-\fBvsearch\fR --cluster_fast \fIqueries.fas\fR --id 0.97 --centroids
+-\fIcentroids.fas\fR --uc \fIclusters.uc\fR
++\fBvsearch\fR \-\-cluster_fast \fIqueries.fas\fR \-\-id 0.97 \-\-centroids
++\fIcentroids.fas\fR \-\-uc \fIclusters.uc\fR
+ .RE
+ .PP
+ Dereplicate the sequences contained in queries.fas, take into account
+@@ -1306,9 +1306,9 @@ to output with the new abundance informa
+ with an abundance of 1:
+ .PP
+ .RS
+-\fBvsearch\fR --derep_fulllength \fIqueries.fas\fR --output
+-\fIqueries_masked.fas\fR --sizein --sizeout --fasta_width 0
+---minuniquesize 2
++\fBvsearch\fR \-\-derep_fulllength \fIqueries.fas\fR \-\-output
++\fIqueries_masked.fas\fR \-\-sizein \-\-sizeout \-\-fasta_width 0
++\-\-minuniquesize 2
+ .RE
+ .PP
+ Mask simple repeats and low complexity regions in the input fasta file
+@@ -1316,26 +1316,26 @@ Mask simple repeats and low complexity r
+ file:
+ .PP
+ .RS
+-\fBvsearch\fR --maskfasta \fIqueries.fas\fR --output
+-\fIqueries_masked.fas\fR --qmask dust
++\fBvsearch\fR \-\-maskfasta \fIqueries.fas\fR \-\-output
++\fIqueries_masked.fas\fR \-\-qmask dust
+ .RE
+ .PP
+ Sort by decreasing abundance the sequences contained in queries.fas
+ (using the "size=\fIinteger\fR" information), relabel the sequences
+-while preserving the abundance information (with --sizeout), keep only
++while preserving the abundance information (with \-\-sizeout), keep only
+ sequences with an abundance equal to or greater than 2:
+ .PP
+ .RS
+-\fBvsearch\fR --sortbysize \fIqueries.fas\fR --output
+-\fIqueries_sorted.fas\fR --relabel sampleA_ --sizeout --minsize 2
++\fBvsearch\fR \-\-sortbysize \fIqueries.fas\fR \-\-output
++\fIqueries_sorted.fas\fR \-\-relabel sampleA_ \-\-sizeout \-\-minsize 2
+ .RE
+ .PP
+ Align all sequences in a database with each other and output all pairwise
+ alignments:
+ .PP
+ .RS
+-\fBvsearch\fR --allpairs_global \fIdatabase.fas\fR
+---alnout \fIresults.aln\fR --acceptall
++\fBvsearch\fR \-\-allpairs_global \fIdatabase.fas\fR
++\-\-alnout \fIresults.aln\fR \-\-acceptall
+ .RE
+ .PP
+ Search queries in a reference database, with a 80%-similarity
+@@ -1343,8 +1343,8 @@ threshold, take terminal gaps into accou
+ similarities:
+ .PP
+ .RS
+-\fBvsearch\fR --usearch_global \fIqueries.fas\fR --db
+-\fIreferences.fas\fR --alnout \fIresults.aln\fR --id 0.8 --iddef 1
++\fBvsearch\fR \-\-usearch_global \fIqueries.fas\fR \-\-db
++\fIreferences.fas\fR \-\-alnout \fIresults.aln\fR \-\-id 0.8 \-\-iddef 1
+ .RE
+ .PP
+ Search a sequence dataset against itself (ignore self hits), get all
+@@ -1352,9 +1352,9 @@ matches with at least 60% identity, and
+ blast-like tab-separated format:
+ .PP
+ .RS
+-\fBvsearch\fR --usearch_global \fIqueries.fas\fR --db
+-\fIqueries.fas\fR --id 0.6 --self --blast6out \fIresults.blast6\fR
+---maxaccepts 0 --maxrejects 0
++\fBvsearch\fR \-\-usearch_global \fIqueries.fas\fR \-\-db
++\fIqueries.fas\fR \-\-id 0.6 \-\-self \-\-blast6out \fIresults.blast6\fR
++\-\-maxaccepts 0 \-\-maxrejects 0
+ .RE
+ .PP
+ Shuffle the input fasta file (change the order of sequences) in a
+@@ -1362,8 +1362,8 @@ repeatable fashion (fixed seed), and wri
+ to the output file:
+ .PP
+ .RS
+-\fBvsearch\fR --shuffle \fIqueries.fas\fR --output
+-\fIqueries_shuffled.fas\fR --seed 13 --fasta_width 0
++\fBvsearch\fR \-\-shuffle \fIqueries.fas\fR \-\-output
++\fIqueries_shuffled.fas\fR \-\-seed 13 \-\-fasta_width 0
+ .RE
+ .PP
+ .\" 
+@@ -1440,17 +1440,17 @@ Bug fixes (ssse3/sse41 requirement, memo
+ Bug fix (now writes help to stdout instead of stderr).
+ .TP
+ .BR v1.0.4\~ "released December 8th, 2014"
+-Added --allpairs_global option. Reduced memory requirements
++Added \-\-allpairs_global option. Reduced memory requirements
+ slightly. Removed memory leaks.
+ .TP
+ .BR v1.0.5\~ "released December 9th, 2014"
+-Fixes a minor bug with --allpairs_global and --acceptall options.
++Fixes a minor bug with \-\-allpairs_global and \-\-acceptall options.
+ .TP
+ .BR v1.0.6\~ "released December 14th, 2014"
+-Fixes a memory allocation bug in chimera detection (--uchime_ref option).
++Fixes a memory allocation bug in chimera detection (\-\-uchime_ref option).
+ .TP
+ .BR v1.0.7\~ "released December 19th, 2014"
+-Fixes a bug in the output from chimera detection with the --uchimeout option.
++Fixes a bug in the output from chimera detection with the \-\-uchimeout option.
+ .TP
+ .BR v1.0.8\~ "released January 22nd, 2015"
+ Introduces several changes and bug fixes:
+@@ -1459,7 +1459,7 @@ Introduces several changes and bug fixes
+ a new linear memory aligner for alignment of sequences longer than
+ 5,000 nucleotides,
+ .IP -
+-a new --cluster_size command that sorts sequences by decreasing
++a new \-\-cluster_size command that sorts sequences by decreasing
+ abundance before clustering,
+ .IP -
+ meaning of userfields qlo, qhi, tlo, thi changed for compatibility
+@@ -1468,12 +1468,12 @@ with usearch,
+ new userfields qilo, qihi, tilo, tihi gives coordinates ignoring
+ terminal gaps,
+ .IP -
+-in --uc output files, a perfect alignment is indicated with a "=" sign,
++in \-\-uc output files, a perfect alignment is indicated with a "=" sign,
+ .IP -
+---cluster_fast will now sort sequences by decreasing length, then by
++\-\-cluster_fast will now sort sequences by decreasing length, then by
+   decreasing abundance and finally by sequence identifier,
+ .IP -
+-default --maxseqlength value set to 50,000 nucleotides,
++default \-\-maxseqlength value set to 50,000 nucleotides,
+ .IP -
+ fix for bug in alignment in rare cases,
+ .IP -
+@@ -1481,7 +1481,7 @@ fix for lack of detection of under- or o
+ .RE
+ .TP
+ .BR v1.0.9\~ "released January 22nd, 2015"
+-Fixes a bug in the function sorting sequences by decreasing abundance (--sortbysize).
++Fixes a bug in the function sorting sequences by decreasing abundance (\-\-sortbysize).
+ .TP
+ .BR v1.0.10\~ "released January 23rd, 2015"
+ Fixes a bug where the sizein option was ignored and always treated as on,


