-
--add-relatives=n (0)
-
--arb-list-fields=FILE
-
--auto-filter-field=name
-
--auto-filter-threshold arg
-
--calc-idty
-
--colors
-
--csv-crlf
-
--csv-id=id (name)
-
--csv-sep=sep (,)
-
--debug-graph
-
--disable-docs
-
--enable-asan
-
--enable-code-coverage
-
--enable-debug
-
--enable-fat-tar
-
--enable-profiling
-
--fasta-block=size
-
--fasta-idx=n
-
--fasta-write-dna
-
--fasta-write-dots
-
--filter=name
-
--fs-cover-gene=n (0)
-
--fs-engine=[internal|pt-server]
-
--fs-full-len=n (1400)
-
--fs-kmer-len=k (10)
-
--fs-kmer-mm=n (0)
-
--fs-kmer-no-fast
-
--fs-kmer-norel
-
--fs-leave-query-out
-
--fs-max=n (40)
-
--fs-min-len=n (150)
-
--fs-min=n (15)
-
--fs-msc-max=id (2)
-
--fs-msc=n (0.7)
-
--fs-no-graph
-
--fs-oldmatch
-
--fs-req-full=n (1)
-
--fs-req-gaps=n (10)
-
--fs-req=n (1)
-
--fs-weight=weight (1)
-
--gene-end=n (0)
-
--gene-start=n (0)
-
--has-cli-vers=cliversion
-
--insertion=[shift|forbid|remove]
-
--intype=[auto|arb|fasta] (auto)
-
--lca-fields=names
-
--lca-quorum=fraction (0.7)
-
--line-length=n (0)
-
--log-file=filename
-
--lowercase=[none|original|unaligned]
-
--markaligned
-
--markcopied
-
--match-score=n (2)
-
--max-in-flight=n (2 * number of CPU cores)
-
--meta-fmt=[none|header|comment|csv]
-
--min-idty=id
-
--mismatch-score=n (-1)
|
-
--no-align
-
--num-pts (1)
-
--orig-db=filename
-
--outtype=[auto|arb|fasta|csv|none] (auto)
-
--overhang=[attach|remove|edge] (attach)
-
--pen-gap=n gap open penalty (5)
-
--pen-gapext=n
-
--prefix=PATH (/usr/local)
-
--preserve-order
-
--prot-level=n (4)
-
--ptdb=filename
-
--ptport=port_or_socket (:/tmp/sina_pt_<pid>)
-
--realign
-
--search-all
-
--search-copy-fields=fields
-
--search-correction=[none|jc] (none)
-
--search-cover=[abs|query|target|min|max|avg|overlap|all|nogap] (query)
-
--search-db=filename (=db)
-
--search-engine=[internal|pt-server]
-
--search-filter-lowercase
-
--search-ignore-super
-
--search-iupac=[pessimistic|*optimistic|exact] (optimistic)
-
--search-kmer-candidates=n (1000)
-
--search-kmer-len=n (10)
-
--search-kmer-mm arg
-
--search-kmer-norel
-
--search-max-result=n (10)
-
--search-min-sim=id (0.7)
-
--search-no-fast don't use fast family search
-
--search-port=port_or_socket (:/tmp/sina_pt2_<pid>)
-
--select-file=filename
-
--select-skip=n (0)
-
--select-step=n (1)
-
--show-conf
-
--show-diff
-
--show-dist
-
--use-subst-matrix
-
--with-arbhome=PATH
-
--with-boost-libdir=PATH
-
--with-boost=PATH
-
--with-buildinfo=TEXT
-
--with-tbb=PATH
-
--write-used-rels
-
-f fields, --fields=fields
-
-h, --help
-
-H, --help-all
-
-i filename, --in=filename (-)
-
-o filename [filename [...]], --out=filename (-)
-
-P, --prealigned
-
-p, --threads (automatic)
-
-q, --quiet
-
-r filename, --db=filename
-
-S, --search
-
-t [all], --turn [=all]
-
-v, --verbose
-
-V, --version
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