Index

Symbols

--add-relatives=n (0) sina command line option --arb-list-fields=FILE sina command line option --auto-filter-field=name sina command line option --auto-filter-threshold arg sina command line option --calc-idty sina command line option --colors sina command line option --csv-crlf sina command line option --csv-id=id (name) sina command line option --csv-sep=sep (,) sina command line option --debug-graph sina command line option --disable-docs configure command line option --enable-asan configure command line option --enable-code-coverage configure command line option --enable-debug configure command line option --enable-fat-tar configure command line option --enable-profiling configure command line option --fasta-block=size sina command line option --fasta-idx=n sina command line option --fasta-write-dna sina command line option --fasta-write-dots sina command line option --filter=name sina command line option --fs-cover-gene=n (0) sina command line option --fs-engine=[internal|pt-server] sina command line option --fs-full-len=n (1400) sina command line option --fs-kmer-len=k (10) sina command line option --fs-kmer-mm=n (0) sina command line option --fs-kmer-no-fast sina command line option --fs-kmer-norel sina command line option --fs-leave-query-out sina command line option --fs-max=n (40) sina command line option --fs-min-len=n (150) sina command line option --fs-min=n (15) sina command line option --fs-msc-max=id (2) sina command line option --fs-msc=n (0.7) sina command line option --fs-no-graph sina command line option --fs-oldmatch sina command line option --fs-req-full=n (1) sina command line option --fs-req-gaps=n (10) sina command line option --fs-req=n (1) sina command line option --fs-weight=weight (1) sina command line option --gene-end=n (0) sina command line option --gene-start=n (0) sina command line option --has-cli-vers=cliversion sina command line option --insertion=[shift|forbid|remove] sina command line option --intype=[auto|arb|fasta] (auto) sina command line option --lca-fields=names sina command line option --lca-quorum=fraction (0.7) sina command line option --line-length=n (0) sina command line option --log-file=filename sina command line option --lowercase=[none|original|unaligned] sina command line option --markaligned sina command line option --markcopied sina command line option --match-score=n (2) sina command line option --max-in-flight=n (2 * number of CPU cores) sina command line option --meta-fmt=[none|header|comment|csv] sina command line option --min-idty=id sina command line option --mismatch-score=n (-1) sina command line option

--no-align sina command line option --num-pts (1) sina command line option --orig-db=filename sina command line option --outtype=[auto|arb|fasta|csv|none] (auto) sina command line option --overhang=[attach|remove|edge] (attach) sina command line option --pen-gap=n gap open penalty (5) sina command line option --pen-gapext=n sina command line option --prefix=PATH (/usr/local) configure command line option --preserve-order sina command line option --prot-level=n (4) sina command line option --ptdb=filename sina command line option --ptport=port_or_socket (:/tmp/sina_pt_<pid>) sina command line option --realign sina command line option --search-all sina command line option --search-copy-fields=fields sina command line option --search-correction=[none|jc] (none) sina command line option --search-cover=[abs|query|target|min|max|avg|overlap|all|nogap] (query) sina command line option --search-db=filename (=db) sina command line option --search-engine=[internal|pt-server] sina command line option --search-filter-lowercase sina command line option --search-ignore-super sina command line option --search-iupac=[pessimistic|*optimistic|exact] (optimistic) sina command line option --search-kmer-candidates=n (1000) sina command line option --search-kmer-len=n (10) sina command line option --search-kmer-mm arg sina command line option --search-kmer-norel sina command line option --search-max-result=n (10) sina command line option --search-min-sim=id (0.7) sina command line option --search-no-fast don't use fast family search sina command line option --search-port=port_or_socket (:/tmp/sina_pt2_<pid>) sina command line option --select-file=filename sina command line option --select-skip=n (0) sina command line option --select-step=n (1) sina command line option --show-conf sina command line option --show-diff sina command line option --show-dist sina command line option --use-subst-matrix sina command line option --with-arbhome=PATH configure command line option --with-boost-libdir=PATH configure command line option --with-boost=PATH configure command line option --with-buildinfo=TEXT configure command line option --with-tbb=PATH configure command line option --write-used-rels sina command line option -f fields, --fields=fields sina command line option -h, --help sina command line option -H, --help-all sina command line option -i filename, --in=filename (-) sina command line option -o filename [filename [...]], --out=filename (-) sina command line option -P, --prealigned sina command line option -p, --threads (automatic) sina command line option -q, --quiet sina command line option -r filename, --db=filename sina command line option -S, --search sina command line option -t [all], --turn [=all] sina command line option -v, --verbose sina command line option -V, --version sina command line option

A

acc field command line option, [1] ali_16s/data field command line option, [1] align_bp_score_slv field command line option, [1] align_cutoff_head_slv field command line option, [1] align_cutoff_tail_slv field command line option, [1] align_family_slv field command line option, [1] align_filter_slv field command line option, [1]

align_ident_slv field command line option, [1] align_log_slv field command line option, [1] align_quality_slv field command line option, [1] align_startpos_slv field command line option, [1] align_stoppos_slv field command line option, [1] aligned_slv field command line option, [1] ARB_color field command line option, [1]

C

configure command line option --disable-docs --enable-asan --enable-code-coverage --enable-debug --enable-fat-tar --enable-profiling --prefix=PATH (/usr/local) --with-arbhome=PATH --with-boost-libdir=PATH --with-boost=PATH --with-buildinfo=TEXT --with-tbb=PATH

F

field command line option ARB_color, [1] acc, [1] ali_16s/data, [1] align_bp_score_slv, [1] align_cutoff_head_slv, [1] align_cutoff_tail_slv, [1] align_family_slv, [1] align_filter_slv, [1] align_ident_slv, [1] align_log_slv, [1] align_quality_slv, [1] align_startpos_slv, [1] align_stoppos_slv, [1] aligned_slv, [1] full_name, [1] name, [1] nearest_slv, [1] nuc, [1] nuc_gene_slv, [1] start, [1] stop, [1] tax_embl, [1] tax_embl_ebi_ena, [1] tax_gg, [1] tax_gtdb, [1] tax_ltp, [1] tax_rdp, [1] tax_slv, [1] used_rels, [1] version, [1]

full_name field command line option, [1]

N

name field command line option, [1] nearest_slv field command line option, [1]

nuc field command line option, [1] nuc_gene_slv field command line option, [1]

S

sina command line option --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 --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 --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 --write-used-rels -H, --help-all -P, --prealigned -S, --search -V, --version -f fields, --fields=fields -h, --help -i filename, --in=filename (-) -o filename [filename [...]], --out=filename (-) -p, --threads (automatic) -q, --quiet -r filename, --db=filename -t [all], --turn [=all] -v, --verbose

start field command line option, [1] stop field command line option, [1]

T

tax_embl field command line option, [1] tax_embl_ebi_ena field command line option, [1] tax_gg field command line option, [1] tax_gtdb field command line option, [1]

tax_ltp field command line option, [1] tax_rdp field command line option, [1] tax_slv field command line option, [1]

U

used_rels field command line option, [1]

V

version field command line option, [1]