menu:Print item:[experimental] Validate taxonomy (SATIVA) itemmethod: (mkdir -p ~/.arb_tmp/sativa_$$; cd ~/.arb_tmp/sativa_$$ ; arb_convert_aln --arb-notify -GenBank TmpInputFile -phylip sativa_in.phy; ${ARB_XCMD} bash -x -c @@LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; arb_sativa.pl $MARKEDONLY $MARKMIS $RANKTEST $VERBOSE $TAXFIELD $TAXCODE $METHOD $NUMREPS $CUTOFF $RANDSEED $CORES $SPECIESFIELD; arb_wait@@; cd ~/.arb_tmp; rm -rf sativa_$$) & seqtype:* itemmeta:V itemhelp:sativa.help #arb_export_tree $TREE > reftree.tre in:TmpInputFile informat:genbank insave: arg:MARKEDONLY arglabel:Process marked species only? argtype:choice_menu argchoice:Yes:--marked-only argchoice:No: arg:MARKMIS arglabel:Mark found misplaced species? argtype:choice_menu argchoice:Yes:--mark-misplaced argchoice:No: arg:RANKTEST arglabel:Test for misplaced higher ranks? argtype:choice_menu argchoice:No: argchoice:Yes:--rank-test arg:TAXFIELD arglabel:Taxonomy path field argtype:text argtext:tax_slv arg:SPECIESFIELD arglabel:Species name field (empty=ignore species) argtype:text argtext:full_name arg:TAXCODE arglabel:Taxonomic code argtype:choice_menu argchoice:Bacteriological:bac argchoice:Botanical:bot argchoice:Zoological:zoo argchoice:Virological:vir arg:METHOD arglabel:Reference tree: inference method argtype:choice_menu argchoice:Thorough (standard RAxML):thorough argchoice:Fast (RAxML "-D" option):fast argchoice:Ultrafast (RAxML "-f e" option):ultrafast arg:NUMREPS arglabel:Reference tree: number of RAxML searches argtype:text argtext:1 arg:CUTOFF arglabel:Confidence cut-off argtype:text argtext:0.51 arg:RANDSEED arglabel:Random seed argtype:text argtext:12345 arg:CORES arglabel:Number of threads to use (0=auto) argtype:text argtext:0 arg:VERBOSE arglabel:Verbose output argtype:choice_menu argchoice:No: argchoice:Yes:--verbose #arg:DUPRANKS #arglabel:Action for non-unique rank names #argtype:choice_menu #argchoice:Ignore:ignore ##argchoice:Auto-rename:autofix #argchoice:Report and exit:abort #argchoice:Skip sequences:skip #arg:BADRANKS #arglabel:Action for redundant ranks (subclass, suborder etc.) #argtype:choice_menu #argchoice:Ignore:ignore ##argchoice:"Best guess" fix:autofix #argchoice:Report and exit:abort #argchoice:Skip sequences:skip