SLiMSuite REST Server documentation site map

pages/:

API Alias FAQ Help News None Tools iuscore missing rlc

docs/:

AAFILE CDICT CMD DATE DATFILE DICT DSVFILE FASFILE FILE FILELIST FOFN FULLPATH GLIST INT INTLIST LIST MOTIFS NUM NUMLIST PATH PERC PPIFILE SEQFILE TDTFILE URL X boolean boolorfile minmax

module/:

tools/:

aphid badasp budapest buscomp comparimotif_V3 depthkopy depthsizer diploidocus fiesta gablam gasp gfessa gopher happi haqesac multihaq numtfinder pafscaff pagsat peptcluster picsi pingu_V3 pingu_V4 presto_V5 qslimfinder saaga samphaser seqmapper seqsuite slimbench slimfarmer slimfinder slimmaker slimmutant slimparser slimprob slimsearch slimsuite smrtscape snapper synbad taxolotl unifake

slimsuite/:

SLiMSuite

libraries/:

ned_eigenvalues ned_rankbydistribution rje rje_aaprop rje_ancseq rje_apollo rje_biogrid rje_blast rje_blast_V1 rje_blast_V2 rje_busco rje_conseq rje_db rje_dismatrix rje_dismatrix_V2 rje_dismatrix_V3 rje_disorder rje_ensembl rje_exonerate rje_forker rje_genbank rje_genecards rje_genemap rje_gff rje_go rje_haq rje_hmm_V1 rje_hpc rje_hprd rje_html rje_iridis rje_kat rje_lrbridge rje_markov rje_mascot rje_mashmap rje_menu rje_mitab rje_motif_V3 rje_motif_stats rje_motiflist rje_motifocc rje_obj rje_paf rje_pam rje_ppi rje_py2 rje_py3 rje_qsub rje_readcore rje_rmd rje_samtools rje_samtools_V0 rje_scoring rje_seq rje_seqlist rje_sequence rje_slim rje_slimcalc rje_slimcore rje_slimhtml rje_slimlist rje_specificity rje_svg rje_synteny rje_taxonomy rje_tm rje_tree rje_tree_group rje_uniprot rje_xgmml rje_xml rje_xref rje_zen snp_mapper

legacy/:

gasp_V1 gopher_V2 pagsat_V1 qslimfinder_V1.9 slimbench_V1 slimdisc_V1.4 slimfinder_V4.9 slimprob_V1.4 smrtscape_V1

extras/:

compass file_monster peptide_dismatrix peptide_stats pic_html prodigis rem_parser rje_dbase rje_glossary rje_itunes rje_mysql rje_pattern_discovery rje_phos rje_pydocs rje_scansite rje_seqgen rje_seqplot rje_sleeper rje_ssds rje_yeast seqforker sfmap2png slim_pickings wormpump

cmd/:

3didsql aadimerfreq aadis aafreq aagapdif aamask aanulldif aaprop abschg absence absmin absminamb absmincut absphasecut absunzipcut ac accfield acclist accnr acconly acctable accuracy addalias addbaits addclass addflanks addimports addlinks addppi addqueries addquery addrand addscore addtags adduni advmax advprob ailmv aliasbackup aliases aliasfile align alignprog allbyall alliso allowvar allquery allreptag allsig alltypes alncut alndir alnext alngap alnprog alnstats alphabet alphahelix alphtabs altcodons altcontext altcontrol altdis altft altkeys altpam altpos altsource alttreatment altupc ambcut ambiguity ambocc analyse analyses analytics aname anchor anchors annotate append approved archived archivedirs aromatic arraydata asscombo assembly assmode association att attributes author autofilter autoload automap autorun autoskip avread backbase background backup backupdb backupdirs backups badX badcloud baddb baddir baddset badgenes badid badppi badtype baits balanced balchg basefile batch batcharg batchbase batchlog batchmode batchout batchrun begfield benchbase benchmark bestmatch bestorf biallelic bigfirst bigindex biogrid biomart blanks blast+path blast2fas blasta blastann blastb blastcf blastcut blastd blastdir blaste blastf blastforce blastg blastgen blasti blasto blastopt blastp blastpath+ blastpath blastprog blastres blastv bootcut bootfilter bootstrap bootstraps bootweight border branchlen buildfile buildpath bycloud bycluster bysmrt calclen calculate calcx calls candidates cardout case casefilter caseft casemask cc2ft cdna cds cdsin cdsonly chaser checkfields checkflanks checknum checkpos checktype checktypes chrmap chromalign chromcov chromspec classcol classify classorder cleandb cleanfiles cleanhaq cleanres cleanup cleardata clearhtml clonemap cloudfix clouds clustalo clustalw clusterfas clusters clustersplit clustertree codons col colbydeg combaits combamb combcut combine combinedfas combineppi comments compare compdb compfilter compile complete complex complexfas compmask compress compresspp concatenate consamb conscore consensi consinfo consmask consout conspec consweight context control controls convert copyright coreal coreic countspec coverage ctlfile custom cutfocus cutstat cwcut cwtree cyscount cysweight cytoscape d damping data datalist datapath datatype datindex datout datpickup dbcomp dbdetails dbdownload dbformat dbindex dblist dbonly dbparse dbprefix dbprocess dbsizes dbsource dbsplit ddi debug deflen degap delimit depend dependhpc depthplot depthsmooth desconly details detailskip dev dimfreq dip diploid dipmode dircut dirdepth direct direction dirlist dirnlen dirsum disdom disgraph disin diskey dismask dismat dismatrix disorder distdir distrees distribute dmidata dmifile dna dnds docdir docsource domainfas domains dombench domfile domfilter domft domino domlink domppi domppidir domtable dormancy dormant dotlocalmin dotplots download dropfields dropout dumpdir edgeswap edit edithome efilter elements elm elmbench elmclass elmdat elmdomains elminstance elminteractors elmpfam email embldat emblpath empai endbuffer endfield endmargin enrcut enrpairs ensdat ensfilter ensgo ensgopath ensloci ensmap enspath enspep enstaxid eorf equiv equivcut equivout errorlog errperbase es est2haq est2rf estgen evalaln evidence exclude expand expandppi expconvert expcut expect experiments exponly extendaa extlist extract extras fakehtml fakemask fam famcut farm farmgablam fasdb fasdir fasid fasout fastapath fastq fastseedx fasttree fdranncut fdrcut featuremask features fetchuid fiestacons filein filelist fileout filexref fillcol filoop filterdir filterout filterself filterseq fisleep fitness fixdown fixendings fixlen fixpam fixup flank flankmask flanks flanksize flatout fluff focus focusocc folder foldindex fontface force forkcmd forkdir forkprog forks forksleep format formatdb fragcov fragfas fragment fragmerge fragrevcomp fragsize frapout fsa ftbest ftfile ftfreq ftgablam ftlist ftmask ftout ftskip ftxcov ftxfreq fudgeft fullblast fullcut fulldoc fullens fullforce fullhgnc fullmap fullnr fulloutput fullpath fullrbh fullref fullres fullscramble fupc fwdonly gablam gablamcut gablamdis gablamfrag gablamo gablamout gabrev gabsim gapblast gapfilter gbatch genbase geneacc genecards geneclass genedata genefield genelist genelists genemap genepickle generate generics genes genesummary genetar genome genomesize genotypes genpath genspec globid gnspacc godata goevidence goexcept gofilter goids gomap goodX gooddb gooddir goodic goodmotif goodppi gopages gopher gopherdir gopherfam goseqdir goslim gosummary gotable graphformats graphtypes grepdat group groupspec gspcode gzip haircut halfhap haq haqbat haqbatch haqdb haqdir haqesac haqmatrix header help hgncdata hgncmap hgnconly hhpid hitdata hitname hitsum hivseq hmm hmmcalibrate hmmerpath hmmoptions hmmout hmmpfam hmmres hmmtab homcut homeback homedir hometitle homfilter homsim hostvirus hpc hpcmode hprd hprdfas hprdpath href html htmlall htmlcss htmldir htmlpath htmlpng htmlstyle hublist hubonly hubs i iccut identifier idfield idlist idmax idmin idsim igap ignore ignoredate ignoreft ignoren ignoreref iini imask include indata indels index indexlen indexre indirect infile info infotext input inputext intact integrity intensity interactive inversedb invmask ioerror iolimit ipilinks ipipath iqtree iridis irun iterate itraq itunes itype iuchdir iucut iumethod iupath iupred iuscoredir jackknife javascript jimdir job jobid jobini join joinmargin joinmerge joinsort keep keepblast keepcase keepfree keeplocal keepnames keepnew keeporder keyid keywords killforks kimura knowns kozak kozwin labels larrow layout lcft legacy lencorrect lenfilter linkout litfile loadbalance loadmatrix local localalnfas localcut localidcut localidmin localmin localsAM localsort localunique locusdir locusout log logfile logfork logint logmask logourl logrem longlink longtdt mafft mailstart mains majcut majdif majfocus majmut majref makeclass makedat makedb makefam makefas makeflyseq makefreq makehmm makehtml makeindex makejim makepages makepng makesnp makespec maketree makeuniprot manpaq mansaq manuals manualurl mapdb mapdir mapdna mapefficiency mapfas mapfields mapfocus mapout mapping mapseq mapspec mapstat maptomany mapxref markov markovx mascot maskcleave masked maskfreq maskft masking maskm maskpickle maskpos masktext matchfix matchic maxaa maxall maxbad maxbin maxcov maxgap maxgapvar maxgapx maxgenes maxglob maxgo maxhyd maxlen maxmutant maxocc maxpara maxpeplen maxrefresh maxseq maxsize maxsup maxupc maxwild maxx mcode meanqc megablam megaslim megaslimdp megaslimfix memfree memsaver mergesplits method methodcap methodfield methodskip metmask mfs mgcfile mgidata minabstag minaln minanchorx minboot mincds minclass mincontiglen mincut mindeg minenrtag minexptag minfamnum minfamsize minfix minfrag minfreq mingo minhapx minhom minic minid minimotif mink minlen minlength minlocid minloclen minmap minmax minmutant minocc minorf minpcov minpep minpeplen minplocid minpoly minpolyat minpos minppi minqn minqv minreadlen minregion minresic minscore minseq minshare minsim minsnp minsum minsup mint mintag mintracks minunique minupc minutr minvcov minvlocid minwild miranda mismatch mismatches missing mitab mixed mode modlinks modpurge modules monophyly monster motalndir motdesc motif motifaln motific motifmask motifout motifs motifseq motinfo motlist msfile msms mst multiclass multicut multihaq muscle musthave mutfield mutfile mutflanks mutpileup mysql name namemap nandr naturaljoin negatives negvpos nematode netchg netphos newacc newchr newgene newheaders newlog newres newscore newupc noamb nobots nocomplex nocontrols nocopyfas nocopylen nocopymerge nodefields nodelist nodemap nodeonly nodes noexec nofork noforks nohits nonaug noneboot noquery normalise normcut normfit noshare nosplice noutr nr nralign nrchoice nrcut nrdb nrfastq nrflanks nrgen nrgene nrid nrkeepann nrmotif nrpep nrsamespec nrseq nrsim nrspec nrstat nsf2nwk nsfin nterm ntrim nudgecyc nwklist obofile obsgo occbench occbenchpos occdata occfile occfilter occonly occres occscale occstats occupc oldblast oldmonster oldpipe oldscores oma omim onetomany optimise ordered orderedfas orfmet orftypes organise orgprefix orphan orphans orth2tdt orthbase orthdb orthid orthspec osx otherfiles outcmd outdir outfile outfmt outformat outlist outmatrix outnames output outstats outstyle overlap overlaps pagan pagehead pairid pairwise palindrome pamcut pamfile pamlpath pammax pamout pamtree paq paqb paqkl paqks paqm parafam paralign parameters paramlist parasplice parent1 parent2 parents parentterms parse parseparam partial password path pathfinder pathqry patisfas pause pdbdata peaksmooth pelm pelmfas pepcount pepcut pepmwt peptalign peptcluster peptdis peptides percentile percres pfam pfamdata pfamout pfandata phasecut phaseindels phbin phenotype phos phosblast phosdat phosres phylip phyoptions picback picdesc picfolder pichome picids pickall pickhead pickid pickle pickledata pickleout picksid pickup pidcheck pileup pillars pingupickle plotft plotre plotstat plotwin plurals pngmax poolcyc poolgen pop1 pop2 pops posinfo positives posmask posmatrix postdup ppcomplex ppexpand ppextra ppi ppibench ppicompile ppid ppidbreport ppidir ppifas ppifile ppiout ppioutdir ppisource ppispec ppisym ppitab ppitype ppn preassembly precall predict prefix prepaq prevbase pridefile pridepath probcut probscore prog program projects protacc protalndir protdesc protdist proteases proteinaln proteins proteome protfield protlist protscores protsummary pround ptmlist pureapi purgelist purify pwenr pwin pylist pypath qassemble qassemblefas qblast qcomplete qconsensus qcover qcut qexact qfasdir qfastacmd qpath qprop qregion qryacc qrygaps qryid qryspec qryvar qseqfile qslimfinder qspec qsub qtype queries query querydb queryfield querynr queryppi queryseq quiet ranbench randat randbase randdesc randfdr randir randmethod randname randnum randomise randppi randreps randres randseed randsource rank rankaln rankfilter ranking rankmeans rankonly rankstat ranktypes rarecut rarrow ratings rds reactome readcheck readfilter readlen recase reciprocal recloud recut reduced redundancy refchr reference refgenome reformat refresh refseq reftype region relcons relconwin release relgappen relwin remhub remlog remslim remsticky rename rep repair replacechar replicate report rerank resave rescale resdir resfile resfiles rest restab restbase restin restout restoutdir restrict restrictid resturl results resume revcompnr reverse revertblastdir revertdir revertnr reviewed rfhits rftran rgraphics rid rjepy rmdirs rna2dna root rootbuffer rpath rq rqfilter rqmean rqstep rsh rst run runfield runid runlist runpath runtypes sampler samples saq saqb saqc saqkl saqks saqm savedis savelocal savespace savetree savetype saveupc savexref scaled scansite scap scapback scavenge scramble scramblecyc screenddi screenelm screenens screenfile screenipi screenmatch screenqry screenrev screenwrap screenx search searchdb searchid searchini sections seedfreq self selfhit selfonly selfsum seqbyseq seqcluster seqdb seqfiles seqfilter seqformat seqgroup seqin seqincmd seqindex seqlen seqmode seqname seqnr seqnum seqocc seqout seqshuffle seqsort seqstats seqtype sequence seqwt serverlist sgd2sp shortutr sigcut signalp sigprime sigv silent simbench simcount simfocus simratios simulate singleseq singlesf singletons sizematch sizesort skipann skipdormant skipgene skipknown skiplist skiploci skipquiet sleep slimbuild slimcalc slimcall slimchance slimcheck slimchg slimcons slimcore slimdesc slimdir slimdisc slimfiles slimfilter slimfold slimhyd slimini slimiup slimjim slimlen slimlencut slimlist slimmaker slimopt slimpath slimppi slimprob slimquery slimranks slimres slimsa slimsearch slimsuite slimsupport slimversion slimwall smearfreq smrtreads smrtunits snapper snpbyftype snpcalc snpdrop snperr snpfile snphead snpkeys snpmap snponly snptabkeys snptable snptableout snptables snptabmap snptype soaplab softmask sortby sorted sortrun sortseq sortxref source sourcedata sourcedate sourcedir sourcepath sourceurl spcode specdat specdup specfile special species speclist specnr speconly specsleep spectable spectdt speedskip splicego splicevar split splitchar splitcsv splitfield splitout splits splitseq splitskip splitzero spokes sqcut sqldump startfrom statfilter sticky stickyhubs stickyppi stiggid strains strand strict stripgap stripnum stripvar students stylepath stylesheets subdir subfolders subjobs subsleep suffix sumfile summarise summaryhgnc svg symmetric symmetry tabber tableonly tabout tagfield tagfile tagindex taglen tagmap tagstart targetcov targeterr targetfield targetxcov targz taxadb taxafield taxalist taxbase taxdir taxfilter taxid taxin taxmap taxonomy taxout tdtfile tdtkeys teiresias teiresiasopt teiresiaspath termini terminorf terms termsplit test testgenes textscale thumbheight thumbnails thumbname tidy tidygap title titletext tmconvert tmhmm tofile tofork tool topblast tophitbuffer tophits tophtml toplist topranks torf toscreen tp track trackprob treatment treeformats trimflank trimtrunc trimx trmode truemarks trunc truncnames truncnt tryparent tuplekeys txt type typefield ucft unifake unifield uniformat unihtml unionly unipath unipaths uniprot uniprotid unique uniquexref unireal unispec unitab unkspec unmatched unzipcut uparse update updatepos uploadsh usealn usebeta usecase usedate usego usegopher usehome usenandr usepos useres usespec usesprot usetrembl useuniprot useweb v validated varlength vbatch vcodes verbose vgablam vgbparse vhost virusdir virusgb vmem vnematrix vspcode vwp wake walltime warn webdir webid webobo webserver webtabs weighted wildscram wildvar win32 winchg windis winhyd winsa winsize winstep wisdoms wtpileup xdir xdivide xgcomplex xgcut xgexpand xgformat xgmml xgmmlatt xhubppi xmargin xmerback xmerfile xmerocc xmers xmerseq xnlist xpad xpaddb xpass xref xrefdata xreflist xreformat xrefout xrefs xreftab xsteplen xtcap xtcut yeast yeastxref zensleep zfilter zscore