NAME

vsearch \-\-allpairs_global — perform global pairwise alignments of all sequence pairs

SYNOPSIS

vsearch \-\-allpairs_global fastafile (\-\-acceptall | \-\-id real) (\-\-alnout | \-\-blast6out | \-\-fastapairs | \-\-matched | \-\-notmatched | \-\-samout | \-\-uc | \-\-userout) filename [options]

DESCRIPTION

The vsearch command --allpairs_global performs optimal global pairwise alignments (Needleman-Wunsch) for all pairs of sequences in a fasta file. Each sequence is compared to all sequences that follow it in the file, for a total of n*(n-1)/2 comparisons where n is the number of sequences.

Sequences are compared on their plus strand only. Either --acceptall (to write all alignments to output) or --id (to set a minimum identity threshold) must be specified. Most accept/reject options from the searching section also apply.

Masking is applied as specified with --qmask and --hardmask.

At least one output option must be specified. This command is multi-threaded.

The --qsegout and --tsegout options do not count as sole output options: when either is used on its own, vsearch rejects the run with “No output files specified”. They can still be used, but only in combination with one of the output options listed in the SYNOPSIS.

To illustrate the comparisons performed on a three-sequence file:

Input:    Pairs compared (n=3, total=3):

>s1       s1 vs s2
AAAA      s1 vs s3
>s2  -->  s2 vs s3
CCCC
>s3
TTTT

OPTIONS

mandatory options

Either --acceptall or --id must be specified, along with at least one output option.

--acceptall
Write the results of all pairwise alignments to output files. Overrides all other accept/reject options, including --id.

--id real
Reject the match if the pairwise identity with the target sequence is lower than real (value ranging from 0.0 to 1.0 included). The pairwise identity is defined by default as (matching columns) / (alignment length - terminal gaps). That definition can be modified with --iddef.

core options

--iddef 0|1|2|3|4
Change the pairwise identity definition used with --id. Accepted values are:

1. CD-HIT definition: (matching columns) / (shortest sequence length).
2. edit distance: (matching columns) / (alignment length).
3. edit distance excluding terminal gaps (default definition for --id).
4. Marine Biological Lab definition, counting each gap opening (internal or terminal) as a single mismatch, whether or not the gap was extended: 1.0 - [(mismatches + gap openings)/(longest sequence length)].
5. BLAST definition, equivalent to --iddef 1 for global pairwise alignments.

--maxaccepts positive integer
Set the maximum number of matching target sequences to accept before stopping the search for a given query. The default value is 1. Use together with --maxrejects. If both --maxaccepts and --maxrejects are set to 0, the complete database is searched.

--maxrejects positive integer
Set the maximum number of non-matching target sequences to consider before stopping the search for a given query. The default value is 32. Use together with --maxaccepts. If both --maxaccepts and --maxrejects are set to 0, the complete database is searched.

--qmask none|dust|soft
Mask regions in query sequences using the dust method or the soft method, or none to suppress masking. Values are case-insensitive, so DUST, Dust, and dust are all accepted. See vsearch-fastx_mask(1) for more details. Warning, when using soft masking, search commands become case sensitive. The default is to mask using dust.

--threads positive integer
Set the number of computation threads to use, from 1 to 1024. The number of threads should not exceed the number of available CPU cores. The default is to use all available cores.

secondary options

--alnout filename
Write pairwise global alignments to filename in a human-readable format. Use --rowlen to set the alignment line width.

--blast6out filename
Write results to filename using a BLAST-like tab-separated format with twelve fields per query-target match: query label, target label, percentage identity, alignment length, mismatches, gap openings, query start, query end, target start, target end, expectation value (always -1), and bit score (always 0). If --output_no_hits is used, non-matching queries are also written. Note that vsearch uses global pairwise alignments, not BLAST’s seed-and-extend algorithm.

--bzip2_decompress
Specify that the input pipe is streaming data compressed using Huffman coding. See bzip2(1) for more details. This option is not needed when reading from a regular file compressed with bzip2.

--fasta_width positive integer
Set the maximal width of sequences when writing fasta files. Longer sequences are folded and written on several lines. Default width is 80 nucleotides. Set to zero (0) to suppress folding.

--fastapairs filename
Write pairwise alignments of query and target sequences to filename, in fasta format.

--gzip_decompress
Specify that the input pipe is streaming data compressed using Lempel-Ziv coding. See gzip(1) for more details. This option is not needed when reading from a regular file compressed with gzip.

--hardmask
Replace masked nucleotides with Ns.

--idprefix positive integer
Reject the sequence match if the first integer nucleotides of the target do not match the query.

--idsuffix positive integer
Reject the sequence match if the last integer nucleotides of the target do not match the query.

--label_suffix string
Add the suffix string to sequence headers when writing fasta or fastq files. For example, with --label_suffix ";status=healthy", sequence header ‘>seq1’ becomes ‘>seq1;status=healthy’.

--leftjust
Reject the sequence match if the pairwise alignment begins with gaps.

--lengthout
Add a sequence length annotation (;length=integer) to each sequence header when writing fasta or fastq files.

--log filename
Write messages to filename. Messages include program version, start and finish times, elapsed time, amount of memory available, maximum amount of memory consumed, number of cores and command line options, and if need be, command-specific informational messages, warnings, and errors.

--matched filename
Write query sequences matching a target sequence to filename, in fasta format.

--maxdiffs positive integer
Reject the sequence match if the alignment contains more than integer substitutions, insertions, or deletions.

--maxgaps positive integer
Reject the sequence match if the alignment contains more than integer insertions or deletions.

--maxhits non-negative integer
Set the maximum number of hits to report once the search is terminated for a given query; hits are sorted by decreasing identity. Unlimited by default, or when the argument is zero. When searching both strands, --maxhits controls the total number of hits reported per query across both strands.

--maxid real
Reject the sequence match if the pairwise identity between the two sequences is greater than real.

--maxqsize positive integer
Reject query sequences with an abundance greater than integer.

--maxqt real
Reject the sequence match if the query/target sequence length ratio is greater than real.

--maxseqlength positive integer
Discard sequences longer than positive integer (50,000 nucleotides by default).

--maxsizeratio real
Reject the sequence match if the query/target abundance ratio is greater than real.

--maxsl real
Reject the sequence match if the shorter/longer sequence length ratio is greater than real.

--maxsubs positive integer
Reject the sequence match if the pairwise alignment contains more than integer substitutions.

--mid real
Reject the sequence match if the pairwise identity, computed ignoring all gaps (internal and terminal), is lower than real.

--mincols positive integer
Reject the sequence match if the alignment length is shorter than integer columns.

--minqt real
Reject the sequence match if the query/target sequence length ratio is lower than real.

--minseqlength positive integer
Discard sequences shorter than positive integer (1 nucleotide by default).

--minsizeratio real
Reject the sequence match if the query/target abundance ratio is lower than real.

--minsl real
Reject the sequence match if the shorter/longer sequence length ratio is lower than real.

--mintsize positive integer
Reject target sequences with an abundance lower than integer.

--minwordmatches non-negative integer
Set the minimum number of k-mer matches required for a sequence to be considered further. The default value is 12 for the default word length of 8. If the argument is 0, no word matches are required.

--n_mismatch
Count alignments of nucleotides against Ns as mismatches.

--no_progress
Suppress the gradually increasing progress indicator normally written to the standard error stderr(3).

--notmatched filename
Write the sequences that were not extracted to filename, in fasta format.

--notrunclabels
Retain whole sequence headers in output files. By default, vsearch truncates sequence headers at first space or tabulation. This option suppresses truncation.

--output_no_hits
Write both matching and non-matching queries to --alnout, --blast6out, --samout, or --userout output files. Non-matching queries are labelled ‘No hits’ in --alnout files.

--qsegout filename
Write the aligned part of each query sequence to filename, in fasta format.

--query_cov real
Reject the sequence match if the fraction of the query aligned to the target is lower than real (value ranging from 0.0 to 1.0 included). Query coverage is computed as (matches + mismatches) / query sequence length, not counting internal or terminal gaps.

--quiet
Suppress messages to the standard output stdout(3) and standard error stderr(3), except for warnings and error messages.

--relabel string
Replace sequence headers with the prefix string and a ticker (1, 2, 3, etc.). For example, with --relabel "cluster:", the first sequence header becomes ‘>cluster:1’, the second sequence header becomes ‘>cluster:2’, and so on. To retain annotations, use their corresponding options (--lengthout, --eeout, and --sizeout). Use --relabel_keep to also retain old sequence identifiers.

--relabel_keep
Retain old sequence identifiers by including them at the end of the new headers, after a space.

--relabel_md5
Replace each sequence header with the MD5 digest derived from the sequence itself. The sequence is converted to upper case, and each ‘U’ is replaced with a ‘T’ before computation of the digest. The MD5 digest is a 128-bit value (16 bytes), represented using a string of 32 ASCII characters. Each pair of characters encodes an hexadecimal value, ranging from x00 to xff. See md5(3) for more details, and --relabel_sha1 for an alternative hashing algorithm. To retain annotations, use their corresponding options (--lengthout, --eeout, and --sizeout). Use --relabel_keep to also retain old sequence identifiers.

--relabel_self
Replace each sequence header with the sequence itself. To retain annotations, use their corresponding options (--lengthout, --eeout, and --sizeout). Use --relabel_keep to also retain old sequence identifiers.

--relabel_sha1
Replace each sequence header with the SHA1 digest derived from the sequence itself. The sequence is converted to upper case, and each ‘U’ is replaced with a ‘T’ before computation of the digest. The SHA1 digest is a 160-bit value (20 bytes), represented using a string of 40 ASCII characters. Each pair of characters encodes an hexadecimal value, ranging from x00 to xff. See sha1(3) for more details, and --relabel_md5 for an alternative hashing algorithm. To retain annotations, use their corresponding options (--lengthout, --eeout, and --sizeout). Use --relabel_keep to also retain old sequence identifiers.

--rightjust
Reject the sequence match if the pairwise alignment ends with gaps.

--rowlen positive integer
Set the width of alignment lines in --alnout output. The default value is 64. Set to 0 to disable line wrapping.

--samheader
Include header lines (@HD, @SQ, @PG) in the SAM file produced by --samout. By default, no header lines are written.

--samout filename
Write alignment results to filename in the SAM format, see vsearch-sam(5). Use --samheader to include header lines. Each non-header line is a SAM record representing either a query-target alignment or the absence of a match. The alignment column of each record uses the CIGAR format, see vsearch-cigar(5).

--sample string
Add the given sample identifier string to sequence headers when writing fasta or fastq files. For instance, if string is ‘ABC’, the text ;sample=ABC will be added to the headers. string is silently truncated at the first ‘;’ or whitespace character (space, tab, newline, carriage return, vertical tab or form feed), so such characters should not be used in string. Other characters (alphabetical, numerical and punctuations) are accepted.

--self
Reject the sequence match if the query and target sequence labels are identical.

--selfid
Reject the sequence match if the query and target sequences are strictly identical.

--sizein
Use the abundance annotations present in sequence headers when reading fasta or fastq file. Search for the pattern [>@;]size=integer[;]. Entries without abundance annotations are silently assumed to be of size=1.

--sizeout
Add abundance annotations to sequence headers when writing fasta or fastq files. Add the pattern ;size=integer. If option --sizein is not used, abundance values are set to 1 for all entries. If --sizein is used, existing abundance annotations are simply reported to output files.

--target_cov real
Reject the sequence match if the fraction of the target sequence aligned to the query is lower than real. Target coverage is computed as (matches + mismatches) / target sequence length, not counting internal or terminal gaps.

--top_hits_only
Report only the hits with the highest pairwise identity for each query.

--tsegout filename
Write the aligned part of each target sequence to filename, in fasta format.

--uc filename
Write pairwise alignment results to filename in a tab-separated uclust-like format with 10 columns. One line is written per alignment (record type always H). Columns are:

1. record type, always H;
2. ordinal number of the target sequence (zero-based);
3. length of the query sequence;
4. percentage of identity with the target;
5. match orientation, always +;
6. not used, always 0;
7. not used, always 0;
8. CIGAR alignment string (M, D, I; = if query and target are identical ignoring terminal gaps); see vsearch-cigar(5);
9. query label;
10. target label.

--userfields string
Select and order the fields written to --userout output. Fields are separated by + (e.g. query+target+id). See vsearch-userfields(7) for a complete description of all available fields.

--userout filename
Write user-defined tab-separated output to filename. Select and order the fields with --userfields.

--weak_id real
Report hits with a pairwise identity of at least real, without stopping the search. Unlike --id, weak hits do not count toward --maxaccepts but do count toward --maxrejects. The value of real must be smaller than the value specified with --id.

--wordlength positive integer
Set the length of words (i.e. k-mers) used for sequence indexing and comparisons. Valid values range from 3 to 15. The default is 8.

--xee
Strip expected error (ee) annotations from sequence headers when writing fasta or fastq files. Search for the pattern [>@;]ee=float[;]. Expected error annotations are added by the synonymous options --fastq_eeout and --eeout described in vsearch-fastx_filter(1).

--xlength
Strip sequence length annotations from sequence headers when writing fasta or fastq files. Search for the pattern [>@;]length=integer[;]. Sequence length annotations are added by the --lengthout option.

--xsize
Strip abundance annotations from sequence headers when writing fasta or fastq files. Search for the pattern [>@;]size=integer[;]. Abundance annotations are added by the --sizeout option.

pairwise alignment options

These options modify the pairwise alignment scoring model. Modify with caution.

--gapext string
Set penalties for a gap extension. See vsearch-pairwise_alignment_parameters(7) for a complete description of the gap penalty declaration system. By default, the penalty is set to 2 for extending internal gaps and to 1 for extending terminal gaps, in both query and target sequences.

--gapopen string
Set penalties for a gap opening. See vsearch-pairwise_alignment_parameters(7) for a complete description of the gap penalty declaration system. By default, the penalty is set to 20 for opening internal gaps and to 2 for opening terminal gaps, in both query and target sequences.

--match integer
Set the score assigned to a match (i.e. equivalent nucleotides) in pairwise alignments. The default value is 2.

--mismatch integer
Set the score assigned to a mismatch (i.e. different nucleotides) in pairwise alignments. The default value is -4.

ignored options

These options are accepted for compatibility with usearch but have no effect.

--band positive integer
This option is ignored. It is provided for compatibility with usearch.

--fulldp
This option is ignored. It is provided for compatibility with usearch. vsearch always uses a full dynamic programming algorithm (Needleman-Wunsch).

--hspw positive integer
This option is ignored. It is provided for compatibility with usearch.

--minhsp positive integer
This option is ignored. It is provided for compatibility with usearch.

--pattern string
This option is ignored. It is provided for compatibility with usearch.

--slots positive integer
This option is ignored. It is provided for compatibility with usearch.

--xdrop_nw positive integer
This option is ignored. It is provided for compatibility with usearch.

EXAMPLES

Compare all pairs in a fasta file and write alignments above 97% identity to a BLAST-like tabular file:

vsearch \
    --allpairs_global sequences.fasta \
    --id 0.97 \
    --blast6out results.tsv

Write all pairwise alignments regardless of identity, using a uclust-like tabular format:

vsearch \
    --allpairs_global sequences.fasta \
    --acceptall \
    --uc results.uc

Compare all pairs and write matching query sequences to a fasta file, using 8 threads:

vsearch \
    --allpairs_global sequences.fasta \
    --id 0.90 \
    --threads 8 \
    --matched matched.fasta \
    --notmatched unmatched.fasta

SEE ALSO

vsearch-usearch_global(1), vsearch-cigar(5), vsearch-fasta(5), vsearch-userfields(7)

CITATION

Rognes T, Flouri T, Nichols B, Quince C, Mahé F. (2016) VSEARCH: a versatile open source tool for metagenomics. PeerJ 4:e2584 doi: 10.7717/peerj.2584

REPORTING BUGS

Submit suggestions and bug-reports at https://github.com/torognes/vsearch/issues, send a pull request on https://github.com/torognes/vsearch, or compose a friendly or curmudgeont e-mail to Torbjørn Rognes (torognes@ifi.uio.no).

AVAILABILITY

Source code and binaries are available at https://github.com/torognes/vsearch.

COPYRIGHT

Copyright (C) 2014-2026, Torbjørn Rognes, Frédéric Mahé and Tomás Flouri

All rights reserved.

Contact: Torbjørn Rognes torognes@ifi.uio.no, Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316 Oslo, Norway

This software is dual-licensed and available under a choice of one of two licenses, either under the terms of the GNU General Public License version 3 or the BSD 2-Clause License.

GNU General Public License version 3

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

The BSD 2-Clause License

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

ACKNOWLEDGMENTS

We would like to thank the authors of the following projects for making their source code available:

• vsearch includes code from Google’s CityHash project by Geoff Pike and Jyrki Alakuijala, providing some excellent hash functions available under a MIT license.
• vsearch includes code derived from Tatusov and Lipman’s DUST program that is in the public domain.
• vsearch includes public domain code written by Alexander Peslyak for the MD5 message digest algorithm.
• vsearch includes public domain code written by Steve Reid and others for the SHA1 message digest algorithm.
• vsearch binaries may include code from the zlib library, copyright Jean-Loup Gailly and Mark Adler.
• vsearch binaries may include code from the bzip2 library, copyright Julian R. Seward.