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Option Type: X

Argument: aagapdif aanulldif absence absmin absminamb absmincut absphasecut absunzipcut accfield acclist addflanks advmax allbyall allreptag alncut alnext alnprog ambcut ambocc analytics assmode author automap avread backbase basefile batcharg batchlog begfield benchbase blasta blastb blastcut blaste blastp blastpath blastprog blastv bootfilter bootstraps border bycloud bycluster casemask chrmap classcol clouds clustersplit combaits combine conscore consweight copyright cutfocus cutstat cwcut d damping datatype dbsource deflen delimit dependhpc depthsmooth dipmode dircut dirdepth direction dirnlen disdom diskey disorder dormancy dotlocalmin edgeswap email endbuffer endfield endmargin enrcut equivcut errperbase evalaln expandppi expcut extras fam famcut farm farmgablam fasid fdranncut fdrcut filoop filterdir fisleep fitness fixpam flank flanks flanksize fluff focusocc fontface forks forksleep fragmerge fragsize fullcut gablamcut gablamfrag gablamo geneacc geneclass genefield genomesize gopages groupspec hitname homcut hometitle homsim hpc hpcmode htmlpng htmlstyle i identifier idmax idmin idsim igap ignore infotext intensity iolimit irun itype iucut iumethod job joinmargin joinmerge joinsort keepfree keyid killforks kozak kozwin layout lcft lenfilter localcut localmin localsort majcut makefam maketree mapefficiency mapfields mapfocus mapspec mapstat markovx masktext matchfix maxaa maxall maxbad maxbin maxcov maxgap maxgapvar maxgapx maxgenes maxglob maxgo maxhyd maxlen maxmutant maxocc maxpara maxpeplen maxrefresh maxseq maxsize maxsup maxupc maxwild maxx meanqc megaslimdp memfree method methodcap mfs minabstag minaln minanchorx minboot mincds minclass mincontiglen mincut mindeg minenrtag minexptag minfix minfrag minfreq mingo minhapx minhom minic minid mink minlen minlocid minloclen minmap minmax minmutant minocc minorf minpcov minpep minpeplen minplocid minpoly minpolyat minpos minppi minqn minqv minreadlen minregion minscore minseq minshare minsim minsnp minsum minsup mintag mintracks minunique minupc minutr minvcov minvlocid minwild mismatch mismatches motdesc motifmask multicut mutfield mutflanks name negvpos newacc newchr newgene nocopylen nocopymerge nodemap nodes noneboot normalise normcut normfit nr nrcut nrflanks nrgene nrid nrsim nrstat ntrim nudgecyc organise orgprefix orthbase orthid orthspec outcmd outfile outformat outmatrix outnames outstats outstyle pagehead pairid pamcut pamfile pammax paqb paqkl paqks paqm password pathfinder pause peaksmooth pepcount pepcut peptalign peptcluster peptdis percentile phasecut phenotype picfolder pickhead picksid pickup plotwin pngmax poolcyc ppexpand ppid ppisource ppn prefix prevbase probcut probscore prog program protacc protfield pwenr qconsensus qcover qcut qfastacmd qprop qryid qtype query queryfield quiet randbase randmethod randname randnum randppi randreps randseed rankaln rankstat rarecut ratings rds refchr reformat refresh reftype relconwin release remhub remsticky rep replicate rerank resave rest restbase resturl resume rftran rootbuffer rqfilter rqstep runid sampler saqb saqc saqkl saqks saqm savespace savetype scramblecyc screenwrap screenx searchid seqformat seqgroup seqincmd seqmode seqname seqnum seqocc seqtype sequence shortutr sigcut simfocus singleseq sizematch sizesort sleep slimcall slimlen slimopt slimranks slimsupport slimversion slimwall smrtreads smrtunits snpcalc snperr sortby sortseq source spcode specdup special species specsleep split splitchar splitfield splits splitseq splitzero sqcut startfrom stiggid strand stripgap subsleep suffix tagfield taglen tagstart targetcov targeterr targetfield targetxcov taxbase teiresias terminorf termsplit textscale thumbheight thumbnails thumbname title topblast tophitbuffer tophits toplist topranks trackprob treatment trimflank trmode trunc truncnames ucft unifield uniformat unzipcut uploadsh v vmem vwp wake walltime winchg windis winhyd winsa winsize winstep wisdoms xdivide xgcut xgexpand xmargin xpad xpaddb xpass xsteplen xtcap xtcut zensleep

Modules: diploidocus extatic gatic humsf09 humsf10 jrj_fastq orcfinder patis prothunter revert rje_1433 rje_aic rje_archive rje_chlamydia rje_embl rje_genomics rje_hm_html rje_mirna rje_misc rje_pacbio rje_paml rje_price rje_slimfungo rje_taxamap samphaser slimdip slimfrap slimgoer slimjim spydarm trex file_monster peptide_dismatrix pic_html prodigis rje_glossary rje_itunes rje_pattern_discovery rje_phos rje_pydocs rje_seqgen rje_seqplot rje_sleeper rje_ssds seqforker slim_pickings gopher_V2 qslimfinder_V1.9 slimbench_V1 slimfinder_V4.9 slimprob_V1.4 rje_aaprop rje_ancseq rje_biogrid rje_blast_V1 rje_blast_V2 rje_blast rje_disorder rje_ensembl rje_forker rje_genbank rje_genecards rje_genemap rje_haq rje_hpc rje_html rje_iridis rje_markov rje_mitab rje_motiflist rje_motif_V3 rje_obj rje_pam rje_ppi rje_qsub rje_samtools_V0 rje_samtools rje_seqlist rje_seq rje_slimcalc rje_slimcore rje_slimhtml rje_slimlist rje_slim rje_synteny rje_taxonomy rje_tm rje_tree rje_uniprot rje rje_xref rje_zen snp_mapper aphid badasp budapest comparimotif_V3 fiesta gablam gfessa gopher happi haqesac multihaq pagsat_V1 pagsat peptcluster picsi pingu_V3 pingu_V4 presto_V5 qslimfinder seqmapper seqsuite slimbench slimfarmer slimfinder slimmaker slimmutant slimparser slimprob slimsearch slimsuite smrtscape_V1 smrtscape snapper unifake

ModuleOptionDescriptionDefault
aphid absence=X Min normalised combined score (arbitrarily assigned to proteins totally absent from samples) 0.5
aphid basefile=X Text base for output files and resdir default based on data file name
aphid combine=X Methods for combining different replicates (max,mean,min,geo,full) mean
aphid enrcut=X Enrichment > X for jack-knifing test 1.0
aphid famcut=X Percentage identity to be used by GABLAM for clustering 0.0
aphid identifier=X Column containing protein indentifications Identifier
aphid intensity=X Column containing intensity values logInt
aphid normalise=X Scoring strategy for normalising intensity (ppm/shared/none/mwt/frag/count) ppm
aphid nr=X Level for redundancy removal (gene/pep/fam) gene
aphid pepcount=X Column containing peptide counts rI
aphid replicate=X Column heading to identify experimntal replicates Replicate
aphid treatment=X Column heading to identify different experimental treatment samples (e.g. condition/control) Treatment
badasp basefile=X Basic 'root' for all files X.* By default will use 'root' of seqin=FILE if given or haq_AccNum if qblast
badasp fam=X minimum number of families (If 0, no subfam grouping) 0
badasp fixpam=X PAM distance fixed to X 100
badasp groupspec=X Species for duplication grouping None
badasp i=X Sets interactivity (-1 for full auto) 0
badasp mfs=X minimum family size 3
badasp pamcut=X Absolute maximum PAM matrix 1000
badasp pammax=X Initial maximum PAM matrix to generate 100
badasp rarecut=X Rare aa cut-off 0.05
badasp v=X Sets verbosity (-1 for silent) 0
badasp xpass=X How many extra passes to make down & up tree after initial GASP 1
budapest basefile=X "Base" name for all results files, e.g. X.budapest.tdt MASCOT file basename
budapest blastcut=X Reduced the number of sequences in HAQESAC runs to X (0 = no reduction) 50
budapest minaln=X Min length of shared region for FIESTA consensus assembly 20
budapest minid=X Min identity of shared region for FIESTA consensus assembly 95.0
budapest minorf=X Min length of ORFs to be considered 10
budapest minpep=X Minimum number of different peptides mapped to final translation/consensus 2
budapest minpolyat=X Min length of poly-A/T to be counted. (-1 = ignore all) 10
budapest newacc=X New base for sequence accession numbers 'BUD'
budapest spcode=X Species code for EST sequences None
budapest topblast=X Report the top X BLAST results 10
comparimotif_V3 ambcut=X Max number of choices in ambiguous position before replaced with wildcard (0=use all) 10
comparimotif_V3 matchfix=X If >0 must exactly match *all* fixed positions in the motifs from: 0
comparimotif_V3 minfix=X Min number of fixed positions for a motif to contain 0
comparimotif_V3 minic=X Min information content for a motif (1 fixed position = 1.0) 2.0
comparimotif_V3 minpep=X Min number of defined positions in a motif 2
comparimotif_V3 minshare=X Min. number of non-wildcard positions for motifs to share 2
comparimotif_V3 mismatches=X <= X mismatches of positions can be tolerated 0
comparimotif_V3 motdesc=X Sets which motifs have description outputs (0-3 as matchfix option) 3
comparimotif_V3 normcut=X Min. normalised MatchIC for motif match 0.5
comparimotif_V3 outstyle=X Sets the output style for the resfile normal
diploidocus lenfilter=X Min read length for filtered subreads 500
diploidocus rqfilter=X Minimum RQ for output subreads 0.84
extatic basefile=X Root name for output files. Path will be stripped and resdir used. * based on cdna or singleseq
extatic mincds=X Minimum CDS lengths to be included in analysis 0
extatic minorf=X Minimum ORF lengths to be considered 0
extatic minutr=X Minimum 5' UTR lengths to be included in analysis 1
extatic nrflanks=X Flanking sequence length (added 5' & 3') for analysing for redundancy within a gene 10
extatic singleseq=X Analyse a single sequence only (named X). cDNA and CDS should be sequence strings. None
fiesta assmode=X Mode to use for EST assembly (nogab,gablam,oneqry) oneqry
fiesta blastcut=X Reduced the number of sequences in HAQESAC runs to X (0 = no reduction) 50
fiesta minaln=X Min length of shared region for consensus assembly 40
fiesta minid=X Min identity of shared region for consensus assembly 95.0
fiesta minorf=X Min length of ORFs to be considered 20
fiesta minpolyat=X Min length of poly-AT to be considered a poly AT 10
fiesta newacc=X New base for sequence accession numbers '' or spcode
fiesta ntrim=X Trims of regions >= X proportion N bases 0.5
fiesta qtype=X Sequence "Type" to be used with NewAcc for annotation of translations hit
fiesta resave=X Number of ESTs to remove before each resave of GABLAM searchdb 200
fiesta spcode=X Species code for EST sequences None
fiesta species=X Species for EST sequences None
file_monster dircut=X Max number of subdirectories to have and still delve into them 50
file_monster dircut=X Max number of subdirectories to have and still delve into them 50
file_monster dirdepth=X Max depth of subdirectories to delve into. Negative = all. -1
file_monster organise=X File reorganisation mode (none/date/month/compile) None
file_monster orgprefix=X Prefix for organised outdir subdirectories ''
file_monster prefix=X Text prefix for new file names
file_monster searchid=X ID for search - allows multiple searches to be compared easily None
file_monster searchid=X ID for search - allows multiple searches to be compared easily None
file_monster sizematch=X Size % similarity threshold to count as match 99.9
file_monster sortby=X Whether to sort by date or name date
gablam addflanks=X Add flanking regions of length X to fragmented hits 0
gablam alncut=X Perform ALIGN pairwise global alignment until < X %ID reached 0
gablam blastb=X Number of hit alignments per query (BLAST -b X) 500
gablam blaste=X E-Value cut-off for BLAST searches (BLAST -e X) 1e-4
gablam blastp=X Type of BLAST search to perform (blastx for DNA vs prot; tblastn for Prot vs DNA) blastp
gablam blastv=X Number of one-line hits per query (BLAST -v X) 500
gablam bycluster=X Generate separate trees and distance matrix for clusters of X+ sequences 0
gablam clustersplit=X Threshold at which clusters will be split (e.g. must be < distance to cluster) 1.0
gablam cutfocus=X Focus for gablamcut. Can be Query/Hit/Either/Both. Either
gablam cutstat=X Stat for gablamcut (eg. AlnLen or OrderedAlnSim. See Function docs for full list) OrderedAlnID
gablam diskey=X GABLAM Output Key to be used for distance matrix 'Qry_AlnID'
gablam dotlocalmin=X Minimum length of local alignment to output to local hit dot plots 1000
gablam evalaln=X Perform ALIGN pairwise global alignment for all hits with e <= X 1000
gablam forks=X Number of parallel sequences to process at once 0
gablam fragmerge=X Max Length of gaps between fragmented local hits to merge 0
gablam gablamcut=X Min. percentage value for a GABLAM stat to report hit (GABLAM from FASTA only) 0.0
gablam gablamfrag=X Length of gaps between mapped residues for fragmenting local hits 0
gablam killforks=X Number of seconds of no activity before killing all remaining forks. 36000
gablam localcut=X Cut-off length for local alignments contributing to global GABLAM stats 0
gablam localmin=X Minimum length of local alignment to output to local stats table 0
gablam localsort=X Local hit field used to sort local alignments for localunique reduction Identity
gablam maxall=X Maximum number of sequences for all-by-all outputs 100
gablam nrcut=X Cut-off for non-redundancy filter, uses nrstat=X for either query or hit 100.0
gablam nrstat=X Stat for nrcut (eg. AlnLen or OrderedAlnSim. See above for full list) OrderedAlnID
gablam outstats=X Whether to output just GABLAM, GABLAMO or All All
gablam rankaln=X Perform ALIGN pairwise global alignment for top X hits 0
gablam reftype=X Whether to map SAM/GFF3 hits onto the Qry, Hit, Both or Combined Hit
gablam startfrom=X Accession number to start from None
gatic flanks=X Length of flanks for profile analysis etc. 20
gatic species=X Species for analysis HUMAN
gfessa allreptag=X Filter out any Tags that are not returned by ALL replicates of X experiments 0
gfessa basefile=X "Base" name for all results files, e.g. X.gfessa.tdt TAG file basename
gfessa enrcut=X Minimum mean fold change between experiments 2.5
gfessa minabstag=X Minimum individual number of counts for a tag to be included (ANY one replicate) 5
gfessa minenrtag=X Minimum number of counts for a tag to be retained for enrichment etc. (summed replicates) 15
gfessa minexptag=X Minimum number of experiments for a tag to be included (no. replicates) 3
gfessa mintag=X Minimum total number of counts for a tag to be included (summed replicates) 0
gfessa mismatch=X No. mismatches to allow. -1 = Exact matching w/o BLAST -1
gfessa normalise=X Method for normalising tag counts within replicate (None/ppm) ppm
gfessa pwenr=X Minimum fold change between pairwise experiment comparisons 1.0
gfessa tagfield=X Field in tagfile containing tag sequence. (All others should be counts) 'Tag sequence'
gfessa taglen=X Length of sequence tags 26
gfessa tagstart=X Sequence starting tags 'CATG'
gopher alnprog=X Choice of alignment program to use (clustalw/clustalo/muscle/mafft/fsa) clustalo
gopher gablamo=X GABLAMO measure to use for similarity measures Sim
gopher maxpara=X Maximum number of paralogues to consider (large gene families can cause problems) 50
gopher minsim=X Minimum %similarity of Query for each "orthologue" 40.0
gopher orthid=X File identifier (Lower case) for orthology files orth
gopher simfocus=X Style of similarity comparison used for MinSim and "Best" sequence identification query
gopher startfrom=X Accession Number / ID to start from. (Enables restart after crash.) None
gopher stiggid=X Base for Stigg ID numbers STIGG
gopher_V2 gablamo=X GABLAMO measure to use for similarity measures Sim
gopher_V2 maxpara=X Maximum number of paralogues to consider (large gene families can cause problems) 50
gopher_V2 minsim=X Minimum %similarity of Query for each "orthologue" 40.0
gopher_V2 simfocus=X Style of similarity comparison used for MinSim and "Best" sequence identification query
gopher_V2 startfrom=X Accession Number / ID to start from. (Enables restart after crash.) None
gopher_V2 stiggid=X Base for Stigg ID numbers STIGG
happi border=X Border setting for tables 0
happi classcol=X Table of "Class" and "Col" (soton$col indexes) to be used for PPI images basefile.col.tdt
happi geneclass=X Field used to identify class of Genes 'Class'
happi genefield=X Field to be used for indentifying Genes 'Gene'
happi gopages=X Create Pages of GO terms with X+ representative genes 5
happi infotext=X Text to display under header 'This data has not yet been published and should not be used without permission.'
happi maxgo=X Go terms above X genes will not have gene data tabs 500
happi pagehead=X Text for Front Page Header 'HAPPI Analysis of basefile'
happi pngmax=X Max number of genes for PNG construction 2000
happi ppexpand=X Expand PPI by X levels for MCODE complex generation 1
haqesac acclist=X Extract only AccNums in list. X can be FILE or list of AccNums X,Y,.. None
haqesac basefile=X Basic 'root' for all files X.* By default will use 'root' of seqin=FILE if given or haq_AccNum if qblast
haqesac blastcut=X Maximum number of sequences to have in dataset (BLAST query against NR dataset.) 0
haqesac blaste=X E-Value cut-off for BLAST searches (BLAST -e X) 1e-4
haqesac blastv=X Number of one-line hits per query (BLAST -v X) 500
haqesac cwcut=X Total number of residues above which to use ClustalW for alignment in place of alnprog=X 0
haqesac d=X Data output level (0-3, see docstring) 1
haqesac fam=X minimum number of families (If 0, no subfam grouping) 0
haqesac fixpam=X PAM distance fixed to X 0
haqesac groupspec=X Species for duplication grouping None
haqesac i=X Sets interactivity (-1 for full auto) 0
haqesac maketree=X Program for making tree None
haqesac maxgap=X Maximum proportion of sequence that may be gaps compared to nearest neighbour (<=0 = No maximum) 0.5
haqesac maxlen=X Maximum length of sequences (<=0 = No maximum) 0
haqesac mfs=X minimum family size 3
haqesac minlen=X Minimum length of sequences 0
haqesac nrid=X %Identity cut-off for Non-Redundancy 99.0
haqesac pairid=X Fasta Alignment ID cut-off for any pair of sequences 0.0
haqesac pamcut=X Absolute maximum PAM matrix 1000
haqesac pammax=X Initial maximum PAM matrix to generate 100
haqesac paqb=X PAQ Block length. 7
haqesac paqkl=X Relative Weighting of keeping Length in PAQ. 1
haqesac paqks=X Relative Weighting of keeping Sequences in PAQ. 3
haqesac paqm=X Min score in PAQ Block (Default matrix: No. residues to match). 3
haqesac qcover=X Min. % (ordered) BLAST coverage of Query vs Hit or Hit vs Query 60.0
haqesac qfastacmd=X Extract query X from qblast database using fastacmd (may also need query=X) None
haqesac qryid=X Fasta Alignment ID with Query cut-off 40.0
haqesac rarecut=X Rare aa cut-off 0.05
haqesac saqb=X SAQ Block length. 10
haqesac saqc=X Min score for a residue in SAQ (Default matrix: no. seqs to share residue). 2
haqesac saqkl=X Relative Weighting of keeping Length in SAQ. 1
haqesac saqks=X Relative Weighting of keeping Sequences in SAQ. 3
haqesac saqm=X No. residues to match in SAQ Block. 7
haqesac specdup=X Minimum number of different species in clade to be identified as a duplication 2
haqesac v=X Sets verbosity (-1 for silent) 0
haqesac xpass=X How many extra passes to make down & up tree after initial GASP 1
humsf09 fdranncut=X FDR cut-off for manual annotation 0.05
humsf10 sigcut=X Significance cut-off for analyses 0.01
jrj_fastq maxbad=X Maximmum number of (internal) bases that can remain below qcut 0
jrj_fastq meanqc=X Minimum mean QC to keep 0.0
jrj_fastq minlen=X Minimum length of sequence that must remain after QC trimming 0
jrj_fastq qcut=X Quality control cut-off. Trim residues below this QC threshold. 20
jrj_fastq qprop=X Proportion of sequence that must remain after QC trimming 0.8
multihaq blastcut=X Restrict HAQESAC and MultiHAQ BLAST searches to top X BLAST hits 0
multihaq multicut=X Restrict MultiHAQ BLASTs to the top X hits from each database (over-rides blastcut) 0
orcfinder blaste=X BLAST e-value threshold for determining relationships 1e=4
orcfinder homcut=X Max number of homologues to allow (to reduce large multi-domain families) 200
orcfinder maxseq=X Maximum number of sequences to process 500
orcfinder maxupc=X Maximum UPC size of dataset to process 0
orcfinder walltime=X Time in hours before program will abort search and exit 1.0
pagsat basefile=X Basename for output files and directories. assembly+ref
pagsat joinmargin=X Number of extra bases allowed to still be considered an end local BLAST hit 10
pagsat joinmerge=X Merging mode for joining chromosomes (mid/start/end/longest) mid
pagsat joinsort=X Whether to sort potential chromosome joins by `Length` or `Identity` Identity
pagsat mincontiglen=X Minimum contig length to retain in assembly (QV filtering only) 1000
pagsat minlocid=X Minimum percentage identity for local hits mapping to chromosome coverage 95.0
pagsat minloclen=X Mininum length for local hits mapping to chromosome coverage 250
pagsat minqv=X Minimum mean QV score for assembly contigs (read from *.qv.csv) 20
pagsat minunique=X Minimum number of "Unique-mapping" nucleotides to retain a contig-chromosome link 250
pagsat newacc=X New base for edited contig accession numbers (None will keep old accnum) None
pagsat newchr=X Code to replace "chr" in new sequence names for additional PAGSAT compatibility ctg
pagsat refchr=X Code used in place of "chr" for reference sequence names chr
pagsat spcode=X Species code for reference genome (if not already processed by rje_genbank) None
pagsat tophitbuffer=X Percentage identity difference to keep best hits for reference genes/proteins. 1.0
pagsat_V1 basefile=X Basename for output files and directories. assembly+ref
pagsat_V1 chrmap=X Contig:Chromosome mapping mode for assembly tidy (unique/align) unique
pagsat_V1 joinmargin=X Number of extra bases allowed to still be considered an end local BLAST hit 10
pagsat_V1 joinmerge=X Merging mode for joining chromosomes (consensus/end) end
pagsat_V1 joinsort=X Whether to sort potential chromosome joins by `Length` or `Identity` Identity
pagsat_V1 mincontiglen=X Minimum contig length to retain in assembly (QV filtering only) 1000
pagsat_V1 minlocid=X Minimum percentage identity for local hits mapping to chromosome coverage 95.0
pagsat_V1 minloclen=X Mininum length for local hits mapping to chromosome coverage 250
pagsat_V1 minqv=X Minimum mean QV score for assembly contigs (read from *.qv.csv) 20
pagsat_V1 newacc=X New base for edited contig accession numbers (None will keep old accnum) None
pagsat_V1 newchr=X Code to replace "chr" in new sequence names for additional PAGSAT compatibility ctg
pagsat_V1 spcode=X Species code for reference genome (if not already processed by rje_genbank) None
pagsat_V1 tophitbuffer=X Percentage identity difference to keep best hits for reference genes/proteins. 1.0
patis basefile=X Leader for *.utr5.fas and *.cds.fas sequences - should start with species Homo_sapiens.GRCh37.p13
patis blaste=X E-value cut-off for BLAST search 1e-10
patis forks=X Number of forks for GABLAM run 0
patis gablamcut=X Percentage identity cut-off for mapping to clones 95.0
patis minfrag=X Minimum length of fragment to clone 303
patis minorf=X Min length of extended ORF 20
patis orthbase=X Basefile for AIC prediction on orthologous species Mus_musculus.NCBIM37.64
patis orthspec=X Species in which to look for conservation etc. of orthologues Mouse
patis ratings=X Which rating scheme to use for AIC (biol2013/jan14) 'jan14'
peptcluster maxgapvar=X Maximum number of consecutive gaps to allow for peptide alignment without Regex guide 3
peptcluster maxgapx=X Maximum total number of gaps to allow for peptide alignment without Regex guide 5
peptcluster outmatrix=X Type for output matrix - tdt / csv / mysql / phylip / png tdt
peptcluster peptalign=T/F/X Align peptides. Will use as guide regular expression, else T/True for regex-free alignment.
peptcluster peptcluster=X Clustering mode (upgma/wpgma/neighbor) upgma
peptcluster peptdis=X Method for generating pairwise peptide distances (id/prop/pam) prop
peptide_dismatrix method=X Peptide Distance Method to use ds_prop
peptide_dismatrix outmatrix=X Type for output matrix - text / mysql / phylip Phylip
pic_html fontface=X Font to use for text Comic Sans MS
pic_html hometitle="X" Title to use for home web page "Photo Page"
pic_html picfolder=X Name of primary folder to look in for photos *
pic_html thumbheight=X Height of thumbnails (pixels) in Preview pages 120
pic_html thumbnails=X Folder containing thumbnails for all pictures of this type thumbnails
pic_html thumbname=X Name to distinguish thumbnails from actual pictures (will rename) _thumb
picsi delimit=X Delimiter for output files tab
pingu_V3 allbyall=X Generates an all-by-all table of PPI links upto X degrees of separation (sample only) 0
pingu_V3 basefile=X Results file prefix if no data file given with data=FILE pingu
pingu_V3 combaits=X Whether to combine bait PPIs into single sample (X) (if addbaits=T)
pingu_V3 fasid=X Text ID for PPI fasta files 'ppi'
pingu_V3 makefam=X GABLAM Percentage identity threshold for grouping sequences into families 0.0
pingu_V3 pathfinder=X Perform (lengthy) PathFinder analysis to link genes upto X degree separation (-1 = no limit) 0
pingu_V3 randnum=X Number of randomisations 1000
pingu_V3 randseed=X Seed for randomiser 0
pingu_V3 remsticky=X Remove "sticky" hubs as defined by >X known PPI 0
pingu_V3 xgexpand=X Expand XGMML network with additional levels of interactors 0
pingu_V4 basefile=X Results file prefix pingu
pingu_V4 fasid=X Text ID for fasta files (*.X.fas) default named after ppisource(+'-dom')
pingu_V4 minppi=X Minimum number of PPI for file output 0
pingu_V4 ppisource=X Source of PPI data. (HINT/FILE) FILE needs 'Hub', 'Spoke' and 'SpokeUni' fields. 'HINT'
pingu_V4 unifield=X Uniprot accession number field identifier for xrefdata 'Uniprot'
presto_V5 alnext=X File extension of alignment files, accnum.X aln.fas
presto_V5 ambcut=X Cut-off for max number of choices in ambiguous position to be shown as variant 10
presto_V5 conscore=X Type of conservation score used: pos
presto_V5 consweight=X Weight given to global percentage identity for conservation, given more weight to closer sequences 0
presto_V5 expcut=X The maximum number of expected occurrences allowed to still search with motif 0
presto_V5 flanksize=X Size of sequence flanks for motifs 30
presto_V5 hitname=X Format for Hit Name: full/short/accnum short
presto_V5 iucut=X Cut-off for IUPred results (0.0 will report mean IUPred score) 0.0
presto_V5 iumethod=X IUPred method to use (long/short) short
presto_V5 matchfix=X If >0 must exactly match *all* fixed positions in the motifs from: 0
presto_V5 minfix=X Min number of fixed positions for a motif to contain 0
presto_V5 minic=X Min information content for a motif (1 fixed position = 1.0) 2.0
presto_V5 minpep=X Min length of motif/peptide X aa 2
presto_V5 minshare=X Min. number of non-wildcard positions for motifs to share 2
presto_V5 motdesc=X Sets which motifs have description outputs (0-3 as matchfix option) 3
presto_V5 outfile=X Base name of results files, e.g. X.presto.tdt. motifsFILE-searchdbFILE.presto.tdt
presto_V5 outstyle=X Sets the output style for the resfile normal
presto_V5 runid=X Adds an additional Run_ID column identifying the run (for multiple appended runs None
presto_V5 startfrom=X Accession Number / ID to start from. (Enables restart after crash.) None
presto_V5 winchg=X Extend charge calculations (if any) to X aa either side of motif 0
presto_V5 windis=X Extend disorder statistic X aa either side of motif (use flanks *only* if negative) 0
presto_V5 winhyd=X Number of aa to extend Eisenberg Hydrophobicity calculation either side of motif 0
presto_V5 winsa=X Number of aa to extend Surface Accessibility calculation either side of motif 0
presto_V5 winsize=X Sets all of the above window sizes (use flanks *only* if negative) 0
presto_V5 xdivide=X Size of dividing Xs between motifs 10
presto_V5 xpad=X Adds X additional Xs to the flanks of the motif (after trimx if trimx=T) 0
presto_V5 xpaddb=X Adds X additional Xs to the flanks of the search database sequences (will mess up alignments) 0
prodigis maxpeplen=X Maximum peptide length to individually return 40
prodigis minpeplen=X Minimum peptide length to consider 0
prodigis pepcut=X Protease used to generate list of identified peptides tryp
prothunter basefile=X This will control output file names and also be used to pick up later analyses for HTML etc.
qslimfinder absmin=X Used if minocc<1 to define absolute min. UP occ 3
qslimfinder absminamb=X Used if ambocc<1 to define absolute min. UP occ 2
qslimfinder ambocc=X Min. UP occurrence for subvariants of ambiguous motifs (minocc if 0 or > minocc) 0.05
qslimfinder blaste=X BLAST e-value threshold for determining relationships 1e=4
qslimfinder casemask=X Mask Upper or Lower case None
qslimfinder clouds=X Identifies motif "clouds" which overlap at 2+ positions in X+ sequences (0=minocc / -1=off) 2
qslimfinder extras=X Whether to generate additional output files (alignments etc.) 1
qslimfinder focusocc=X Motif must appear in X+ focus groups (0 = all) 0
qslimfinder homcut=X Max number of homologues to allow (to reduce large multi-domain families) 0
qslimfinder maxseq=X Maximum number of sequences to process 500
qslimfinder maxupc=X Maximum UPC size of dataset to process 0
qslimfinder maxwild=X Maximum number of consecutive wildcard positions to allow 2
qslimfinder minic=X Minimum information content for returned motifs 2.1
qslimfinder minocc=X Minimum number of unrelated occurrences for returned SLiMs. (Proportion of UP if < 1) 0.05
qslimfinder minwild=X Minimum number of consecutive wildcard positions to allow 0
qslimfinder motifmask=X List (or file) of motifs to mask from input sequences
qslimfinder probcut=X Probability cut-off for returned motifs 0.1
qslimfinder probscore=X Score to be used for probability cut-off and ranking (Prob/Sig) Sig
qslimfinder runid=X Run ID for resfile (allows multiple runs on same data) DATE:TIME
qslimfinder savespace=0 Delete "unneccessary" files following run (best used with targz): 0
qslimfinder sizesort=X Sorts batch files by size prior to running (+1 small->big; -1 big->small; 0 none) 0
qslimfinder slimlen=X Maximum length of SLiMs to return (no. non-wildcard positions) 5
qslimfinder topranks=X Will only output top X motifs meeting probcut 1000
qslimfinder walltime=X Time in hours before program will abort search and exit 1.0
qslimfinder_V1.9 absmin=X Used if minocc<1 to define absolute min. UP occ 3
qslimfinder_V1.9 absminamb=X Used if ambocc<1 to define absolute min. UP occ 2
qslimfinder_V1.9 ambocc=X Min. UP occurrence for subvariants of ambiguous motifs (minocc if 0 or > minocc) 0.05
qslimfinder_V1.9 blaste=X BLAST e-value threshold for determining relationships 1e=4
qslimfinder_V1.9 casemask=X Mask Upper or Lower case None
qslimfinder_V1.9 clouds=X Identifies motif "clouds" which overlap at 2+ positions in X+ sequences (0=minocc / -1=off) 2
qslimfinder_V1.9 extras=X Whether to generate additional output files (alignments etc.) 1
qslimfinder_V1.9 focusocc=X Motif must appear in X+ focus groups (0 = all) 0
qslimfinder_V1.9 homcut=X Max number of homologues to allow (to reduce large multi-domain families) 0
qslimfinder_V1.9 maxseq=X Maximum number of sequences to process 500
qslimfinder_V1.9 maxupc=X Maximum UPC size of dataset to process 0
qslimfinder_V1.9 maxwild=X Maximum number of consecutive wildcard positions to allow 2
qslimfinder_V1.9 minic=X Minimum information content for returned motifs 2.1
qslimfinder_V1.9 minocc=X Minimum number of unrelated occurrences for returned SLiMs. (Proportion of UP if < 1) 0.05
qslimfinder_V1.9 minwild=X Minimum number of consecutive wildcard positions to allow 0
qslimfinder_V1.9 motifmask=X List (or file) of motifs to mask from input sequences
qslimfinder_V1.9 probcut=X Probability cut-off for returned motifs 0.1
qslimfinder_V1.9 probscore=X Score to be used for probability cut-off and ranking (Prob/Sig) Sig
qslimfinder_V1.9 runid=X Run ID for resfile (allows multiple runs on same data) DATE:TIME
qslimfinder_V1.9 savespace=0 Delete "unneccessary" files following run (best used with targz): 0
qslimfinder_V1.9 sizesort=X Sorts batch files by size prior to running (+1 small->big; -1 big->small; 0 none) 0
qslimfinder_V1.9 slimlen=X Maximum length of SLiMs to return (no. non-wildcard positions) 5
qslimfinder_V1.9 topranks=X Will only output top X motifs meeting probcut 1000
qslimfinder_V1.9 walltime=X Time in hours before program will abort search and exit 1.0
revert blaste=X BLAST evalue cut-off 1e-10
revert farmgablam=X Whether to run a pre-REVERT farming of batch BLAST searches using X forks each 0
revert gablamfrag=X Length of gaps between mapped residues for fragmenting local hits 100
revert minpcov=X Min. %coverage for viral proteins during NR reduction 40.0
revert minplocid=X Min. local %identity for viral proteins during NR reduction 30.0
revert minvcov=X Min. %coverage for viral genomes during NR reduction 40.0
revert minvlocid=X Min. local %identity for viral genomes during NR reduction 30.0
rje delimit=X Sets standard delimiter for results output files \t
rje forks=X Number of parallel sequences to process at once 0
rje i=X Sets interactivity (-1 for full auto) 0
rje killforks=X Number of seconds of no activity before killing all remaining forks. 36000
rje maxbin=X Maximum number of trials for using binomial (else use Poisson) -
rje rest=X Variable that sets the output to be returned by REST services None
rje v=X Sets verbosity (-1 for silent) 0
rje_1433 sqcut=X Sequest score cutoff. Scores must be greater than or equal to this 0.95
rje_1433 xtcap=X XTandem score cap ("Best" X-Tandem score) -10
rje_1433 xtcut=X XTandem score cutoff. Scores must be less than or equal to this -2.5
rje_aaprop aagapdif=X Property difference given to amino acid vs gap comparisons 5
rje_aaprop aanulldif=X Property difference given to amino acid vs null values (e.g. X) 0.5
rje_aic flank=X Length for 5' flanking sequence 1000
rje_aic kozak=X Basename for Kozak analysis input 'Homo_sapiens.GRCh37.56'
rje_aic kozwin=X No. of nucleotides either side of start codon 21
rje_aic nrgene=X Which gene type to use for redundancy removal (Gene/EnsG) 'Gene'
rje_aic rep=X Number of random replicates 1000
rje_aic shortutr=X 5' UTR 10
rje_ancseq fixpam=X\t PAM distance fixed to X 0
rje_ancseq rarecut=X\t Rare aa cut-off 0.05
rje_ancseq xpass=X\t How many extra passes to make down & up tree after initial GASP 1
rje_archive dormancy=X Min number of days of inactivity before a directory gets rated as dormant (0=no dormancy) 30
rje_archive quiet=X Min number of days of inactivity before a directory gets rates as quiet 1
rje_archive rds=X UNSW_RDS project code to use (e.g. D0234444)
rje_archive uploadsh=X Full path for runnining upload.sh script '/share/apps/unswdataarchive/2015-09-10/upload.sh'
rje_biogrid dbsource=X Source database (biogrid/dip/intact/mint/reactome) biogrid
rje_biogrid minseq=X Minimum number of PPI sequences in order to output fasta file 3
rje_biogrid species=X Name of species to use data for (will be read from file if BioGRID) human
rje_blast blasta=X Number of processors to use (BLAST -a X) 1
rje_blast blastb=X Number of hit alignments per query (BLAST -b X) 250
rje_blast blaste=X E-Value cut-off for BLAST searches (BLAST -e X) 1e-4
rje_blast blastp=X BLAST program (BLAST -p X) blastp
rje_blast blastpath=X path for blast files c:/bioware/blast/
rje_blast blastv=X Number of one-line hits per query (BLAST -v X) 500
rje_blast gablamfrag=X Length of gaps between mapped residue for fragmenting local hits 100
rje_blast localcut=X Cut-off length for local alignments contributing to global GABLAM stats) 0
rje_blast_V1 blasta=X Number of processors to use (BLAST -a X) 1
rje_blast_V1 blastb=X Number of hit alignments per query (BLAST -b X) 250
rje_blast_V1 blaste=X E-Value cut-off for BLAST searches (BLAST -e X) 1e-4
rje_blast_V1 blastp=X BLAST program (BLAST -p X) blastp
rje_blast_V1 blastpath=X path for blast files ''
rje_blast_V1 blastv=X Number of one-line hits per query (BLAST -v X) 500
rje_blast_V1 gablamfrag=X Length of gaps between mapped residue for fragmenting local hits 100
rje_blast_V1 localcut=X Cut-off length for local alignments contributing to global GABLAM stats) 0
rje_blast_V2 blasta=X Number of processors to use (BLAST -a X) 1
rje_blast_V2 blastb=X Number of hit alignments per query (BLAST -b X) 500
rje_blast_V2 blaste=X E-Value cut-off for BLAST searches (BLAST -e X) 1e-4
rje_blast_V2 blastprog=X BLAST program to use. blastp=X also recognised. (BLAST -p X) blastp
rje_blast_V2 blastv=X Number of one-line hits per query (BLAST -v X) 500
rje_blast_V2 fragmerge=X Max Length of gaps between fragmented local hits to merge 0
rje_blast_V2 gablamfrag=X Length of gaps between mapped residue for fragmenting local hits 100
rje_blast_V2 localcut=X Cut-off length for local alignments contributing to global GABLAM stats) 0
rje_blast_V2 qconsensus=X Whether to convert QAssemble alignments to consensus sequences (None/Hit/Full) None
rje_blast_V2 reftype=X Whether to map SAM/GFF3 hits onto the Qry, Hit, Both or Combined Hit
rje_blast_V2 tophits=X Sets max number of BLAST hits returned (blastb and blastv) 500
rje_chlamydia winsize=X Window size for NT composition plots 5000
rje_chlamydia winstep=X Window step size for NT composition plots 1000
rje_disorder disorder=X Disorder method to use (iupred/foldindex/anchor/parse) iupred
rje_disorder filoop=X Number of times to try connecting to FoldIndex server 10
rje_disorder fisleep=X Number of seconds to sleep between attempts 2
rje_disorder iucut=X Cut-off for IUPred/ANCHOR results 0.2
rje_disorder iumethod=X IUPred method to use (long/short) short
rje_disorder minregion=X Minimum length of an ordered/disordered region 0
rje_disorder name=X Name of sequence to predict disorder for
rje_disorder sequence=X Sequence to predict disorder for (autorun)
rje_embl lcft=X Feature to add for LowerCase portions of sequence
rje_embl outformat=X Format for generated DAT file (uniprot/embl) embl
rje_embl ucft=X Feature to add for UpperCase portions of sequence
rje_ensembl automap=X Minimum value of mapstat for mapping to occur 80.0
rje_ensembl mapstat=X GABLAM Stat to use for mapping assessment (ID/Sim/Len) ID
rje_ensembl mingo=X Minumum number of genes to output GO category 0
rje_ensembl resume=X Species or species code to pickup run from None
rje_ensembl specsleep=X Sleep for X seconds between species downloads 60
rje_forker forks=X Number of parallel sequences to process at once 0
rje_forker forksleep=X Sleep time (seconds) between cycles of forking out more process 0
rje_forker iolimit=X Limit of number of IOErrors before termination 50
rje_forker killforks=X Number of seconds of no activity before killing all remaining forks. 36000
rje_forker memfree=X Min. proportion of node memory to be free before spawning new fork 0.1
rje_genbank geneacc=X Feature detail to use for gene sequence accession number (added to details) locus_tag
rje_genbank protacc=X Feature detail to use for protein sequence accession number (added to details) protein_id
rje_genbank spcode=X Overwrite species read from file (if any!) with X None
rje_genecards species=X Species to output in table Human
rje_genemap basefile=X Root for output files genemap
rje_genemap keyid=X Key field header to be used in main Data dictionary - aliases map to this Symbol
rje_genomics begfield=X Field for beginning position QryStart
rje_genomics endfield=X Field for end position HitStart
rje_genomics queryfield=X Field defining the Query ("Read") name Qry
rje_genomics reformat=X Output format (GFF3/SAM) GFF3
rje_genomics targetfield=X Field defining the Target (Genome contig) name Hit
rje_glossary copyright=X Copyright statement for page 'RJ Edwards 2012'
rje_glossary htmlstyle=X Output HTML style for splits (tab/table/h3) h3
rje_glossary name=X Title for HTML output 'Glossary'
rje_glossary splits=X Number of sets to divide terms into 6
rje_glossary termsplit=X Text to use for splitting term from description (if file extension not recognised) tab
rje_haq paqb=X PAQ Block length. 7
rje_haq paqkl=X Relative Weighting of keeping Length in PAQ. 1
rje_haq paqks=X Relative Weighting of keeping Sequences in PAQ. 3
rje_haq paqm=X No. residues to match in PAQ Block. 3
rje_haq saqb=X SAQ Block length. 10
rje_haq saqc=X Min no. seqs to share residue in SAQ. 2
rje_haq saqkl=X Relative Weighting of keeping Length in SAQ. 1
rje_haq saqks=X Relative Weighting of keeping Sequences in SAQ. 3
rje_haq saqm=X No. residues to match in SAQ Block. 7
rje_hm_html border=X Border setting for tables 0
rje_hpc basefile=X Base for output files - compiled from individual run results None
rje_hpc farm=X Program to farm out using seqbyseq mode.
rje_hpc hpcmode=X Mode to be used for farming jobs between nodes (rsh/fork) fork
rje_hpc iolimit=X Limit of number of IOErrors before termination 50
rje_hpc keepfree=X Number of processors to keep free on head node 1
rje_hpc memfree=X Min. proportion of node memory to be free before spawning job 0.0
rje_hpc pickhead=X Header to extract from OutList file and used to populate AccNum to skip
rje_hpc startfrom=X Sequence ID at which to begin the SeqBySeq farming None
rje_hpc subsleep=X Sleep time (seconds) between cycles of subbing out jobs to hosts 1
rje_html analytics=X Google Analytics code to use with pages
rje_html border=X Border setting for tables 0
rje_html copyright=X Copyright statement for page 'RJ Edwards 2015'
rje_html title=X Default title for HTML page
rje_iridis basefile=X Base for output files - compiled from individual run results None
rje_iridis iolimit=X Limit of number of IOErrors before termination 50
rje_iridis irun=X Exectute a special iRun analysis on Iridis (gopher/slimfinder/qslimfinder/slimsearch/unifake)
rje_iridis keepfree=X Number of processors to keep free on head node 1
rje_iridis memfree=X Min. proportion of node memory to be free before spawning job 0.0
rje_iridis pickup=X Header to extract from OutList file and used to populate AccNum to skip
rje_iridis pickup=X Header to extract from OutList file and used to populate AccNum to skip
rje_iridis runid=X Text identifier for iX run None
rje_iridis subsleep=X Sleep time (seconds) between cycles of subbing out jobs to hosts 1
rje_itunes mintracks=X Min. number of tracks for averages 1
rje_itunes toplist=X Number of entries to feature in HTML top lists 20
rje_markov direction=X Direction to read chains (fwd/bwd/both) fwd
rje_markov negvpos=X Perform Negatives versus Positives analysis on X.* files None
rje_mirna maxseq=X Maximum number of sequences to process 500
rje_mirna minmax=X Minimum value for Maximum expression value 1.0
rje_misc job=X Identifier for the job to be performed None
rje_mitab dbsource=X Source database for evidence field 'mitab'
rje_mitab unifield=X Uniprot accession number field identifier for xrefdata 'Uniprot'
rje_motif_V3 ambcut=X Cut-off for max number of choices in ambiguous position to be shown as variant (0=All) 10
rje_motiflist alnext=X File extension of alignment files, accnum.X aln.fas
rje_motiflist ambcut=X Cut-off for max number of choices in ambiguous position to be shown as variant 10
rje_motiflist conscore=X Type of conservation score used: pos
rje_motiflist consweight=X Weight given to global percentage identity for conservation, given more weight to closer sequences 0
rje_motiflist flanksize=X Size of sequence flanks for motifs 30
rje_motiflist iucut=X Cut-off for IUPred results (0.0 will report mean IUPred score) 0.0
rje_motiflist iumethod=X IUPred method to use (long/short) short
rje_motiflist minfix=X Min number of fixed positions for a motif to contain 0
rje_motiflist minic=X Min information content for a motif (1 fixed position = 1.0) 2.0
rje_motiflist minpep=X Min length of motif/peptide X aa 2
rje_motiflist percentile=X Percentile steps to return in addition to mean 0
rje_motiflist winchg=X Extend charge calculations (if any) to X aa either side of motif 0
rje_motiflist windis=X Extend disorder statistic X aa either side of motif (use flanks *only* if negative) 0
rje_motiflist winhyd=X Number of aa to extend Eisenberg Hydrophobicity calculation either side of motif 0
rje_motiflist winsa=X Number of aa to extend Surface Accessibility calculation either side of motif 0
rje_motiflist winsize=X Sets all of the above window sizes (use flanks *only* if negative) 0
rje_motiflist xdivide=X Size of dividing Xs between motifs 10
rje_obj delimit=X Sets standard delimiter for results output files \t
rje_obj forks=X Number of parallel sequences to process at once 0
rje_obj i=X Sets interactivity (-1 for full auto) 0
rje_obj killforks=X Number of seconds of no activity before killing all remaining forks. 36000
rje_obj maxbin=X Maximum number of trials for using binomial (else use Poisson) -
rje_obj rest=X Variable that sets the output to be returned by REST services None
rje_obj screenwrap=X Maximum width for some screen outputs 200
rje_obj v=X Sets verbosity (-1 for silent, 0 for no progress counters) 1
rje_pacbio avread=X Average read length (bp) 20000
rje_pacbio errperbase=X Error-rate per base 0.14
rje_pacbio genomesize=X Genome size (bp) 0
rje_pacbio mapefficiency=X [Adv.] Efficiency of mapping anchor subreads onto seed reads for correction 1.0
rje_pacbio maxcov=X Maximmum X coverage to calculate 100
rje_pacbio minanchorx=X Minimum X coverage for anchor subreads 6
rje_pacbio rqstep=X Size of RQ jumps for calculation (min 0.001) 0.01
rje_pacbio smrtreads=X Average assemble output of a SMRT cell 50000
rje_pacbio smrtunits=X Units for smrtreads=X (reads/Gb/Mb) reads
rje_pacbio targetcov=X Target percentage coverage for final genome 99.999
rje_pacbio targeterr=X Target errors per base for preassembly 1/genome size
rje_pacbio targetxcov=X Target 100% X Coverage for pre-assembly 3
rje_pacbio xmargin=X "Safety margin" inflation of X coverage 1
rje_pacbio xsteplen=X [Adv.] Size (bp) of increasing coverage steps for calculating required depths of coverage 1e6
rje_pam pamcut=X Absolute maximum PAM matrix 1000
rje_pam pamfile=X Sets PAM1 input file jones.pam
rje_pam pammax=X Initial maximum PAM matrix to generate 100
rje_paml basefile=X Base for names of results files 'pamlres'
rje_paml stripgap=X Strip codons with gaps in at least X sequences 2
rje_pattern_discovery delimit=X Text delimiter \\t
rje_pattern_discovery igap=X Information Content "Gap penalty" (wildcard penalisation) 0
rje_pattern_discovery maxsup=X Max. number of sequences to have in file 0
rje_pattern_discovery minsup=X Min. number of sequences to have in file 3
rje_pattern_discovery remhub=X If X > 0.0, removes "hub" protien ("HUB_PPI") and any proteins >=X% identity to hub 0.0
rje_pattern_discovery slimcall="X" Call for SLiMDisc in batch mode. May have leading commands. "python slimdisc_V1.4.py"
rje_pattern_discovery slimopt="X" Text string of additional SLiMDisc options ""
rje_pattern_discovery slimranks=X Return top X SLiMDisc ranked sequences 1000
rje_pattern_discovery slimsupport=X Min. SLiMDisc support (-S X). If < 1, it is a proportion of input dataset size. 0.1
rje_pattern_discovery slimversion=X Version of SLiMDisc to run (See slimcall=X for batch file jobs) 1.4
rje_pattern_discovery slimwall=X TEIRESIAS walltime (minutes) in SLiMDisc run (-W X) 60
rje_phos homsim=X Percentage identity (GABLAM; phosblast qry) for marking as homologue 40.0
rje_phos idsim=X Percentage identity (GABLAM; phosblast qry) for marking as identity 95.0
rje_ppi damping=X Force Directed Layout, damping parameter 0.9
rje_ppi expandppi=X Expand reduced Node list by X PPI levels 0
rje_ppi fluff=X MCODE "fluff" threshold. <0 = No Fluff 0.5
rje_ppi fragsize=X Combine smaller fragments upto fragsize 200
rje_ppi layout=X Layout to be used for XGMML output spring
rje_ppi mindeg=X MCODE min degree for node scoring 2
rje_ppi minfrag=X Minimum fragment size to keep 3
rje_ppi mink=X MCODE min k-core values 2
rje_ppi nodemap=X Try to map Nodes first using Node table field X
rje_ppi nudgecyc=X Number of cycles between node nudges (try to bump out of unstable equilibria) 1000
rje_ppi vwp=X MCODE vertex weighting percentage 0.2
rje_ppi walltime=X Walltime (hours) for layouts 0.02
rje_price fitness=X Fitness measurement cons
rje_price normfit=X Normalise fitness to have mean of 1 False
rje_price phenotype=X Phenotype measurement cons
rje_price query=X Identifier of query sequence None
rje_price seqgroup=X Sequence grouping method triplets
rje_price special=X Instigate special run, e.g. allbyall None
rje_pydocs author=X Author name to put at bottom of webpages RJ Edwards
rje_pydocs email=X E-Mail address for general contact seqsuite@gmail.com
rje_pydocs methodcap=X Maximum number of method calls before collapsed to single line 0
rje_pydocs name=X Name for PyDoc run. Used for file naming and within documentation files. 'pydocs'
rje_pydocs release=X Release for packages YYYY-MM-DD
rje_qsub dependhpc=X Name of HPC system for depend 'blue30.iridis.soton.ac.uk'
rje_qsub email=X Email address to email job stats to at end ''
rje_qsub hpc=X Name of HPC system for depend 'IRIDIS4'
rje_qsub job=X Name of job file (.job added) qsub
rje_qsub nodes=X Number of nodes to run on 4
rje_qsub pause=X Wait X seconds before attempting showstart 5
rje_qsub ppn=X Processors per node 12
rje_qsub program=X Program call for Qsub (and options) None
rje_qsub vmem=X Virtual Memory limit for run (GB) 48
rje_qsub walltime=X Walltime for qsub job (hours) 60
rje_samtools absmincut=X Absolute minimum read count for minor allele (used if mincut<1) 2
rje_samtools basefile=X Basename for frequency comparison output .v.
rje_samtools depthsmooth=X Smooth out any read plateaus < X nucleotides in length 200
rje_samtools dirnlen=X Include directional read length data at X bp intervals (readlen=T; 0=OFF) 500
rje_samtools fdrcut=X Additional FDR cutoff for enriched treatment SNPs 1.0
rje_samtools fullcut=X Proportion of read to be mapped to count as full-length 0.9
rje_samtools majcut=X Frequency cutoff for Major allele 0.0
rje_samtools mincut=X Minimum read count for minor allele (proportion if <1) 1
rje_samtools minqn=X Min. number of reads meeting qcut (QN) for output 10
rje_samtools peaksmooth=X Smooth out Xcoverage peaks < X depth difference to flanks (<1 = %Median) 0.05
rje_samtools qcut=X Min. quality score for a call to include 30
rje_samtools sigcut=X Significance cutoff for enriched treatment SNPs 0.05
rje_samtools_V0 minfreq=X Minor allele(s) frequency correction for zero counts (e.g. Sequencing error) 0.001
rje_samtools_V0 qcut=X Min. quality score for a call to include 40
rje_seq alnprog=X Choice of alignment program to use (clustalw/clustalo/muscle/mafft/fsa/pagan) clustalo
rje_seq maxgap=X Maximum proportion of sequence that may be gaps (<=0 = No maximum) 0
rje_seq maxglob=X Maximum proportion of sequence predicted to be ordered (<=0 = None; >=1 = Absolute) 0
rje_seq maxlen=X Maximum length of sequences (<=0 = No maximum) 0
rje_seq maxx=X Maximum proportion of sequence that may be Xs (<=0 = No maximum; >=1 = Absolute no.) 0
rje_seq minlen=X Minimum length of sequences 0
rje_seq minorf=X Minimum ORF length for a DNA/EST translation (reformatting only) 0
rje_seq minpoly=X Minimum length of poly-A tail for 3rf / 6rf EST translation (reformatting only) 20
rje_seq nrid=X %Identity cut-off for Non-Redundancy (GABLAMO) 100.0
rje_seq nrsim=X %Similarity cut-off for Non-Redundancy (GABLAMO) None
rje_seq ntrim=X Trims of regions >= X proportion N bases (X residues for protein) 0.0
rje_seq query=X Selects query sequence by name None
rje_seq relconwin=X Window size for relative conservation scoring 30
rje_seq seqname=X Output sequence names for PNG files etc. (short/Name/Number/AccNum/ID) short
rje_seq seqtype=X Force program to read as DNA, RNA, Protein or Mixed (case insensitive; read=Will work it out) None
rje_seq trunc=X Truncates each sequence to the first X aa. (Last X aa if -ve) (Useful for webservers like SingalP.) 0
rje_seqgen idmax=X Max number for randseq ID. If < seqnum, will use seqnum. If <0, no zero-prefixing of IDs. 0
rje_seqgen idmin=X Starting numerical ID for randseq (allows appending) 1
rje_seqgen markovx=X Order of markov chain to use for sequence construction 1
rje_seqgen maxhyd=X Maximum mean hydrophobicity score 10
rje_seqgen poolcyc=X Number of times to retry making sequences if rules are broken 1
rje_seqgen randname=X Name 'leader' for output fasta file randseq
rje_seqgen scramblecyc=X Number of attempts to try each scramble before giving up 10000
rje_seqgen screenx=X Reject generated sequences containing screened Xmers >= X 0
rje_seqgen seqnum=X Number of random sequences to generate 24
rje_seqgen teiresias=X Length of patterns to be screened by additional TEIRESIAS search on scrambled vs original 0
rje_seqlist maxlen=X Maximum length of sequences (<=0 = No maximum) 0
rje_seqlist minlen=X Minimum sequence length 0
rje_seqlist minorf=X Min. ORF length for translated sequences output. -1 for single translation inc stop codons -1
rje_seqlist newacc=X New base for sequence accession numbers - will rename sequences None
rje_seqlist newgene=X New gene for renamed sequences (if blank will use newacc or 'seq' if none read) None
rje_seqlist reformat=X Output format for sequence files (fasta/short/acc/acclist/speclist/index/dna2prot/peptides/(q)region/revcomp) fasta
rje_seqlist rftran=X No. reading frames (RF) into which to translate (1,3,6) 1
rje_seqlist sampler=N(,X) Generate (X) file(s) sampling a random N sequences from input into seqout.N.X.fas 0
rje_seqlist seqformat=X Expected format of sequence file None
rje_seqlist seqmode=X Sequence mode, determining method of sequence storage (full/list/file/index/db/filedb). file
rje_seqlist seqtype=X Sequence type (prot(ein)/dna/rna/mix(ed)) None
rje_seqlist sortseq=X Whether to sort sequences prior to output (size/invsize/accnum/name/seq/species/desc) None
rje_seqlist spcode=X Species code for non-gnspacc format sequences None
rje_seqlist split=X String to be inserted between each concatenated sequence ''
rje_seqlist splitseq=X Split output sequence file according to X (gene/species) None
rje_seqlist terminorf=X Min. length for terminal ORFs, only if no minorf=X ORFs found (good for short sequences) -1
rje_seqplot outfile=X Leader for output files None
rje_seqplot plotwin=X Window for stats plot +/- 7
rje_sleeper sleep=X Seconds to sleep for between prints 600 (10 mins)
rje_sleeper wake=X Total seconds until finishing 864,000 (10 days)
rje_slim ambcut=X Cut-off for max number of choices in ambiguous position to be shown as variant (0=All) 10
rje_slimcalc alnext=X File extension of alignment files, AccNum.X (checked before Gopher used) orthaln.fas
rje_slimcalc conscore=X Type of conservation score used: rlc
rje_slimcalc consweight=X Weight given to global percentage identity for conservation, given more weight to closer sequences 0
rje_slimcalc iucut=X Cut-off for IUPred results (0.0 will report mean IUPred score) 0.0
rje_slimcalc iumethod=X IUPred method to use (long/short) short
rje_slimcalc minhom=X Minimum number of homologues for making conservation score 1
rje_slimcalc percentile=X Percentile steps to return in addition to mean 0
rje_slimcalc relconwin=X Window size for relative conservation scoring 30
rje_slimcalc winsize=X Used to define flanking regions for calculations. If negative, will use flanks *only* 0
rje_slimcore blaste=X BLAST e-value threshold for determining relationships 1e=4
rje_slimcore casemask=X Mask Upper or Lower case None
rje_slimcore equivcut=X BLOSUM score cut-off for equivalence groups 1
rje_slimcore homcut=X Max number of homologues to allow (to reduce large multi-domain families) 0
rje_slimcore masktext=X Text ID to over-ride automated masking text and identify specific masking settings None
rje_slimcore maxseq=X Maximum number of sequences to process 0
rje_slimcore maxupc=X Maximum UPC size of dataset to process 0
rje_slimcore megaslimdp=X Accuracy (d.p.) for MegaSLiM masking tool raw scores 4
rje_slimcore motifmask=X List (or file) of motifs to mask from input sequences
rje_slimcore randbase=X Base for random dataset name rand
rje_slimcore savespace=0 Delete "unneccessary" files following run (best used with targz): 0
rje_slimcore sizesort=X Sorts batch files by size prior to running (+1 small->big; -1 big->small; 0 none) 0
rje_slimcore walltime=X Time in hours before program will abort search and exit 1.0
rje_slimfungo minocc=X Min occurrences for a motif in a GO category 6
rje_slimhtml border=X Border setting for tables 0
rje_slimhtml xgcut=X Significance cut-off for XGMML 0.01
rje_slimlist alnext=X File extension of alignment files, accnum.X aln.fas
rje_slimlist ambcut=X Cut-off for max number of choices in ambiguous position to be shown as variant 10
rje_slimlist flanksize=X Size of sequence flanks for motifs 30
rje_slimlist iucut=X Cut-off for IUPred results (0.0 will report mean IUPred score) 0.0
rje_slimlist iumethod=X IUPred method to use (long/short) short
rje_slimlist minfix=X Min number of fixed positions for a motif to contain 0
rje_slimlist minic=X Min information content for a motif (1 fixed position = 1.0) 0.0
rje_slimlist minpos=X Min number of defined positions 0
rje_slimlist percentile=X Percentile steps to return in addition to mean 0
rje_slimlist winsize=X Used to define flanking regions for stats. If negative, will use flanks *only* 0
rje_slimlist xdivide=X Size of dividing Xs between motifs 10
rje_ssds strand=X Strand for RACE primers -1 (3'), 1 (5') or 0 (both) 0
rje_synteny tophitbuffer=X Percentage identity difference to keep best hits for reference genes/proteins. 1.0
rje_taxamap basefile=X Base for output files. Will reuse unless force=T 'taxmap'
rje_taxamap bootfilter=X Filter bootstrap support < X to "Uncertain" 0.0
rje_taxamap minboot=X Minimum bootstrap value for an "in-clade" with query protein 0.5
rje_taxamap minclass=X Convert taxa with score < minclass to "Other" for *.CLASS.tdt output 1.0
rje_taxamap minscore=X Filter out species codes with score < minscore 1.0
rje_taxamap minsum=X Convert taxa with score < minsum to "Other" for *.taxsum.tdt output 10.0
rje_taxamap noneboot=X Bootstrap support to give "None" ratings 1.0
rje_taxamap taxbase=X Base of previous run to load results from, if not basefile
rje_taxonomy basefile=X Results file prefix. Will use first taxin=LIST term if missing None
rje_tm source=X Source text for mySQL file 'tmhmm'
rje_tree bootstraps=X Number of bootstraps 0
rje_tree deflen=X Default branch length (when none given, also for tree scaling) 0.1
rje_tree fam=X minimum number of families (If 0, no subfam grouping) 0
rje_tree groupspec=X Species for duplication grouping None
rje_tree maketree=X Program for making tree None
rje_tree mfs=X minimum family size 3
rje_tree outnames=X 'short'/'long' names in output file short
rje_tree rootbuffer=X Min. distance from node for root placement (percentage of branch length) 0.1
rje_tree savetype=X Format for generated tree file (nsf/nwk/text/r/png/bud/qspec/cairo/te/svg/html) nwk
rje_tree specdup=X Minimum number of different species in clade to be identified as a duplication 1
rje_tree textscale=X Default scale for text trees (no. of characters per deflen distance) 4
rje_tree truncnames=X Truncate names to X characters (0 for no truncation) 123
rje_uniprot accfield=X Accession number field for acctable=FILE extraction UniProt
rje_uniprot basefile=X If set, can use "T" or "True" for other `*out` options. (Will default to `datout` if given) None
rje_uniprot lcft=X Feature to add for LowerCase portions of sequence
rje_uniprot specsleep=X Sleep for X seconds between species downloads 60
rje_uniprot ucft=X Feature to add for UpperCase portions of sequence
rje_uniprot uniformat=X Desired UniProt format for URL download (over-rules normal processing). Append gz to compress. txt
rje_xref basefile=X Basefile for output files Default: filexref or first xrefdata input file w/o path
rje_xref keyid=X Key field header to be used in main Data dictionary - aliases map to this 'Gene'
rje_xref mapfields=X Fields to be used for Alias mapping plus KeyID. (Must be in XRef).
rje_xref splitchar=X Character on which to split fields for multiple alias processing '|'
rje_zen wisdoms=X Number of Zen Wisdoms to return 10
rje_zen zensleep=X Time in seconds to sleep between wisdoms 0
samphaser absmincut=X Absolute minimum read count for minor allele (used if mincut<1) 2
samphaser absphasecut=X Absolute minimum read count for phasecut (used if phasecut<1) 5
samphaser absunzipcut=X Absolute minimum read count for unzipcut (used if unzipcut<1) 3
samphaser endmargin=X Extend block ends within X nucleotides of sequence ends 10
samphaser mincut=X Minimum read count for minor allele (proportion of QN if <1) for pileup parsing 0.1
samphaser minhapx=X Minimum mean coverage for haplotig 5
samphaser minsnp=X Min number of SNPs per phased haplotype block 5
samphaser phasecut=X Minimum read count for minor allele for phasing (proportion of QN if <1) 0.25
samphaser snpcalc=X Max number of SNPs to use for read probability calculations (fewer = quicker) 10
samphaser snperr=X Probability of an incorrect (biallelic) SNP call for individual read nucleotides 0.05
samphaser splitzero=X Whether to split haplotigs at zero-coverage regions of X+ bp (-1 = no split) 100
samphaser trackprob=X Min probability for assigning a read/SNP to Track A/B 0.95
samphaser unzipcut=X Minimum read count for allele for unzipping haplotigs (proportion of QN if <1) 0.1
seqforker forks=X Number of parallel sequences to process at once 0
seqforker i=X Sets interactivity (-1 for full auto) 0
seqforker killforks=X Number of seconds of no activity before killing all remaining forks. 3600
seqforker outcmd=X Command line option for giving output file name. Will be altered to match forked splits (*.*) None
seqforker seqincmd=X Command given to program for input file name seqin=
seqforker split=X Number of sequences per split file 0
seqforker startfrom=X Will pick up program at this sequence, where X is the name or accession number None
seqforker v=X Sets verbosity (-1 for silent) 0
seqmapper automap=X Minimum value of mapstat for automatic mapping to occur (if i<1) 99.5
seqmapper blaste=X E-Value cut-off for BLAST searches (BLAST -e X) 1e-4
seqmapper blastv=X Number of BLAST hits to return per query (BLAST -v X) 20
seqmapper delimit=X Delimiter for *.mapping.* file (will set extension) tab
seqmapper i=X Set interactivity. i=-1 full auto. i=0 no menu. i=1 interactive menu. 1
seqmapper mapfocus=X Focus for mapping statistic, i.e. which sequence must meet requirements query
seqmapper mapspec=X Maps sequences onto given species code. "Self" = same species as query. "None" = any. None
seqmapper mapstat=X GABLAM Stat to use for mapping assessment (if GABLAM in mapping list) (ID/Sim/Len) ID
seqmapper minmap=X Minimum value of mapstat for any mapping to occur 90.0
seqmapper startfrom=X Shortname or AccNum of seqin file to startfrom (will append results) (memsaver=T only) None
seqsuite batcharg=X Commandline argument to use for batchrun files 'seqin'
seqsuite batchlog=X Generate separate basefile.X log files for each batch run file (None for single log) log
seqsuite prog=X Identifies the tool to be used. Will load defaults from X.ini (before seqsuite.ini) seqlist
slim_pickings advmax=X Max number of sequences to use computationally intensive advanced probability 35
slim_pickings alnext=X File extension of alignment files, accnum.X orthaln.fas
slim_pickings delimit=X Change delmiter to X ,
slim_pickings flanksize=X Size of sequence flanks for motifs 30
slim_pickings iucut=X Cut-off for IUPred results 0.2
slim_pickings iumethod=X IUPred method to use (long/short) short
slim_pickings percentile=X Percentile steps to return in addition to mean 0
slim_pickings picksid=X Outputs an extra 'PicksID' column containg the identifier X
slim_pickings rankstat=X Stat to use to re-rank data RScore
slim_pickings rerank=X Re-ranks according to RScore (if expect=T) and only outputs top X new ranks (if > 0) 5000
slim_pickings slimranks=X Maximum number of SlimDisc ranks to exract from any given dataset 5000
slim_pickings slimversion=X SLiMDisc results version for compiled output 1.4
slim_pickings windis=X Number of aa to extend disorder prediction each side of occurrence 0
slim_pickings winhyd=X Number of aa to extend Eisenberg Hydrophobicity calculation either side of motif 0
slim_pickings winsa=X Number of aa to extend Surface Accessibility calculation either side of motif 0
slim_pickings xdivide=X Size of dividing Xs between motifs 10
slimbench benchbase=X Basefile for SLiMBench benchmarking output slimbench
slimbench bycloud=X Whether to compress results into clouds prior to assessment (True/False/Both) Both
slimbench datatype=X Type of data to be generated and/or benchmarked (occ/elm/ppi/dom/sim/simonly) elm
slimbench filterdir=X Directory suffix for filtered benchmarking datasets _Filtered/
slimbench itype=X Interaction identifer for PPI datasets first element of ppisource
slimbench maxseq=X Maximum number of randsource sequences for SLiM to hit (also maxaa and maxupc limits) 1000
slimbench minic=X Min information content for a motif (1 fixed position = 1.0) 2.0; 1.1 for OccBench
slimbench minupc=X Minimum number of UPC for benchmark dataset 3
slimbench ppid=X PPI source protein identifier type (gene/uni/none; will work out from headers if None) None
slimbench ppisource=X Source of PPI data. (See documentation for details.) (HINT/FILE) 'HINT'
slimbench randbase=X Base for random dataset name if simbench=F ran
slimbench randreps=X Number of replicates for each random (or simulated) datasets 8
slimbench_V1 benchbase=X Basefile for SLiMBench benchmarking output slimbench
slimbench_V1 bycloud=X Whether to compress results into clouds prior to assessment (True/False/Both) Both
slimbench_V1 datatype=X Type of data to be generated and/or benchmarked (elm/sim/simonly) elm
slimbench_V1 minic=X Min information content for a motif (1 fixed position = 1.0) 2.0
slimbench_V1 minupc=X Minimum number of UPC for ELM dataset True
slimbench_V1 randbase=X Base for random dataset name if simulate=F ran
slimbench_V1 randreps=X Number of replicates for each random (or simulated) datasets 10
slimdip dipmode=X Run mode for SLiMDip (slimdip/mimicry/enrichment/legacy) slimdip
slimdip edgeswap=X Number of times to swap edges (x edge number) for edge swap method 10
slimdip randbase=X This is the base of the randbase.X.tdt shuffled PPI files BASEFILE.rand
slimdip randmethod=X Method for randomisation (shuffle/edgeswap) shuffle
slimdip randppi=X Number of random PPI datasets to generate for enrichment analysis 1000
slimdip runid=X RunID for SLiMProb run. (Can also extract from SLiMProb occ.csv file SLiMDIP
slimfarmer basefile=X Set the log, RunID, ResFile, ResDir and Job to X None
slimfarmer dependhpc=X Name of HPC system for depend 'blue30.iridis.soton.ac.uk'
slimfarmer email=X Email address to email job stats to at end ''
slimfarmer farm=X Execute a special SLiMFarm analysis on HPC batch
slimfarmer forks=X Number of forks to be used when hpcmode=fork and qsub=F. 1
slimfarmer hpc=X Name of HPC system 'katana'
slimfarmer hpcmode=X Mode to be used for farming jobs between nodes (rsh/fork) fork
slimfarmer iolimit=X Limit of number of IOErrors before termination 50
slimfarmer job=X Name of job file (.job added) slimfarmer
slimfarmer keepfree=X Number of processors to keep free on head node 1
slimfarmer memfree=X Min. proportion of node memory to be free before spawning job 0.1
slimfarmer nodes=X Number of nodes to run on 1
slimfarmer pause=X Wait X seconds before attempting showstart 5
slimfarmer pickhead=X Header to extract from OutList file and used to populate AccNum to skip
slimfarmer ppn=X Processors per node 16
slimfarmer runid=X Text identifier for SLiMSuite job farming `job`
slimfarmer subsleep=X Sleep time (seconds) between cycles of subbing out jobs to hosts 1
slimfarmer vmem=X Virtual Memory limit for run (GB) 126
slimfarmer walltime=X Walltime for qsub job (hours) 12
slimfinder absmin=X Used if minocc<1 to define absolute min. UP occ 3
slimfinder absminamb=X Used if ambocc<1 to define absolute min. UP occ 2
slimfinder ambocc=X Min. UP occurrence for subvariants of ambiguous motifs (minocc if 0 or > minocc) 0.05
slimfinder blaste=X BLAST e-value threshold for determining relationships 1e=4
slimfinder casemask=X Mask Upper or Lower case None
slimfinder clouds=X Identifies motif "clouds" which overlap at 2+ positions in X+ sequences (0=minocc / -1=off) 2
slimfinder extras=X Whether to generate additional output files (alignments etc.) 1
slimfinder focusocc=X Motif must appear in X+ focus groups (0 = all) 0
slimfinder homcut=X Max number of homologues to allow (to reduce large multi-domain families) 0
slimfinder maxseq=X Maximum number of sequences to process 500
slimfinder maxupc=X Maximum UPC size of dataset to process 0
slimfinder maxwild=X Maximum number of consecutive wildcard positions to allow 2
slimfinder minic=X Minimum information content for returned motifs 2.1
slimfinder minocc=X Minimum number of unrelated occurrences for returned SLiMs. (Proportion of UP if < 1) 0.05
slimfinder minwild=X Minimum number of consecutive wildcard positions to allow 0
slimfinder motifmask=X List (or file) of motifs to mask from input sequences
slimfinder probcut=X Probability cut-off for returned motifs (sigcut=X also recognised) 0.1
slimfinder probscore=X Score to be used for probability cut-off and ranking (Prob/Sig/S/R) Sig
slimfinder randbase=X Base for random dataset name rand
slimfinder runid=X Run ID for resfile (allows multiple runs on same data) DATE
slimfinder savespace=0 Delete "unneccessary" files following run (best used with targz): 0
slimfinder sizesort=X Sorts batch files by size prior to running (+1 small->big; -1 big->small; 0 none) 0
slimfinder slimlen=X Maximum length of SLiMs to return (no. non-wildcard positions) 5
slimfinder topranks=X Will only output top X motifs meeting probcut 1000
slimfinder walltime=X Time in hours before program will abort search and exit 1.0
slimfinder_V4.9 absmin=X Used if minocc<1 to define absolute min. UP occ 3
slimfinder_V4.9 absminamb=X Used if ambocc<1 to define absolute min. UP occ 2
slimfinder_V4.9 ambocc=X Min. UP occurrence for subvariants of ambiguous motifs (minocc if 0 or > minocc) 0.05
slimfinder_V4.9 blaste=X BLAST e-value threshold for determining relationships 1e=4
slimfinder_V4.9 casemask=X Mask Upper or Lower case None
slimfinder_V4.9 clouds=X Identifies motif "clouds" which overlap at 2+ positions in X+ sequences (0=minocc / -1=off) 2
slimfinder_V4.9 extras=X Whether to generate additional output files (alignments etc.) 1
slimfinder_V4.9 focusocc=X Motif must appear in X+ focus groups (0 = all) 0
slimfinder_V4.9 homcut=X Max number of homologues to allow (to reduce large multi-domain families) 0
slimfinder_V4.9 maxseq=X Maximum number of sequences to process 500
slimfinder_V4.9 maxupc=X Maximum UPC size of dataset to process 0
slimfinder_V4.9 maxwild=X Maximum number of consecutive wildcard positions to allow 2
slimfinder_V4.9 minic=X Minimum information content for returned motifs 2.1
slimfinder_V4.9 minocc=X Minimum number of unrelated occurrences for returned SLiMs. (Proportion of UP if < 1) 0.05
slimfinder_V4.9 minwild=X Minimum number of consecutive wildcard positions to allow 0
slimfinder_V4.9 motifmask=X List (or file) of motifs to mask from input sequences
slimfinder_V4.9 probcut=X Probability cut-off for returned motifs (sigcut=X also recognised) 0.1
slimfinder_V4.9 probscore=X Score to be used for probability cut-off and ranking (Prob/Sig/S/R) Sig
slimfinder_V4.9 randbase=X Base for random dataset name rand
slimfinder_V4.9 runid=X Run ID for resfile (allows multiple runs on same data) DATE
slimfinder_V4.9 savespace=0 Delete "unneccessary" files following run (best used with targz): 0
slimfinder_V4.9 sizesort=X Sorts batch files by size prior to running (+1 small->big; -1 big->small; 0 none) 0
slimfinder_V4.9 slimlen=X Maximum length of SLiMs to return (no. non-wildcard positions) 5
slimfinder_V4.9 topranks=X Will only output top X motifs meeting probcut 1000
slimfinder_V4.9 walltime=X Time in hours before program will abort search and exit 1.0
slimfrap fdranncut=X FDR cut-off for manual annotation 0.05
slimgoer maxgenes=X Maximum number of genes for a GO term to apply to 2000
slimgoer minhom=X Minimum number of homologues for each protein 3
slimgoer minocc=X Minimum number of occurrences for a given Motif/GO combo 5
slimjim htmlpng=X Graphic for corner of header frames - links back to Home 'SBS_100.png'
slimjim name=X Name of analysis 'SLiMFinder Human PPI Analysis'
slimjim suffix=X Suffix added to gene symbols for dataset name .ppi
slimmaker ignore=X Amino acid(s) to ignore. (If nucleotide, would be N-) 'X-'
slimmaker maxaa=X Max. no. different amino acids for one position 5
slimmaker minfreq=X Min. combined freq of accepted aa to avoid wildcard 0.75
slimmaker minseq=X Min. no. of sequences for an aa to be in 3
slimmaker peptalign=T/F/X Align peptides. Will use as guide regular expression, else T/True for regex-free alignment. True
slimmutant maxmutant=X Maximum number of mutants for output 100000
slimmutant minmutant=X Minimum number of mutants for output 100
slimmutant mutfield=X Field in mutfile corresponding to AA subsitution data 'AAChange'
slimmutant mutflanks=X Generate for casemask=Upper of X aa flanking mutation (None if < 1) 0
slimmutant ppisource=X Source of PPI data. (HINT/FILE) FILE needs 'Hub' and 'SpokeUni' fields. 'HINT'
slimmutant protfield=X Field in mutfile corresponding to protein accession number 'Uniprot'
slimmutant runid=X Limit analysis to SLiMProb RunID (blank = analyse all)
slimmutant splitfield=X Field in mutfile to split data on (saved as basefile.X.tdt)
slimparser maxrefresh=X Maximum number of seconds for incrementing check refresh 600
slimparser password=X Optional password for REST jobid retrieval None
slimparser refresh=X Initial number of seconds for between checks for job status (will double) 5
slimparser rest=X Return text for just the REST output element X
slimparser restbase=X Basefile for parsed REST output that lacks defined filename jobid
slimparser resturl=X URL of rest server 'http://rest.slimsuite.unsw.edu.au/'
slimprob blaste=X BLAST e-value threshold for determining relationships 1e=4
slimprob casemask=X Mask Upper or Lower case None
slimprob extras=X Whether to generate additional output files (alignments etc.) 2
slimprob maxocc=X Filter out Motifs with more than maximum number of occurrences 0
slimprob maxseq=X Maximum number of sequences to process 0
slimprob maxsize=X Maximum dataset size to process in AA (or NT) 100,000
slimprob motifmask=X List (or file) of motifs to mask from input sequences
slimprob savespace=0 Delete "unneccessary" files following run (best used with targz): 0
slimprob seqocc=X Restrict to sequences with X+ occurrences (adjust for high frequency SLiMs) 1
slimprob walltime=X Time in hours before program will abort search and exit 1.0
slimprob_V1.4 blaste=X BLAST e-value threshold for determining relationships 1e=4
slimprob_V1.4 casemask=X Mask Upper or Lower case None
slimprob_V1.4 extras=X Whether to generate additional output files (alignments etc.) 2
slimprob_V1.4 maxocc=X Filter out Motifs with more than maximum number of occurrences 0
slimprob_V1.4 maxseq=X Maximum number of sequences to process 0
slimprob_V1.4 maxsize=X Maximum dataset size to process in AA (or NT) 100,000
slimprob_V1.4 motifmask=X List (or file) of motifs to mask from input sequences
slimprob_V1.4 savespace=0 Delete "unneccessary" files following run (best used with targz): 0
slimprob_V1.4 seqocc=X Restrict to sequences with X+ occurrences (adjust for high frequency SLiMs) 1
slimprob_V1.4 walltime=X Time in hours before program will abort search and exit 1.0
slimsearch blaste=X BLAST e-value threshold for determining relationships 1e=4
slimsearch casemask=X Mask Upper or Lower case None
slimsearch extras=X Whether to generate additional output files (alignments etc.) 1
slimsearch maxocc=X Filter out Motifs with more than maximum number of occurrences 0
slimsearch maxseq=X Maximum number of sequences to process 0
slimsearch maxsize=X Maximum dataset size to process in AA (or NT) 100,000
slimsearch motifmask=X List (or file) of motifs to mask from input sequences
slimsearch savespace=0 Delete "unneccessary" files following run (best used with targz): 0
slimsearch seqocc=X Restrict to sequences with X+ occurrences (adjust for high frequency SLiMs) 1
slimsearch walltime=X Time in hours before program will abort search and exit 1.0
slimsuite prog=X Identifies the tool to be used. Will load defaults from X.ini (before slimsuite.ini) help
smrtscape avread=X Average read length (bp) 20000
smrtscape errperbase=X Error-rate per base 0.14
smrtscape lenfilter=X Min read length for filtered subreads 5000
smrtscape mapefficiency=X Efficiency of mapping anchor subreads onto seed reads for correction 0.8
smrtscape maxcov=X Maximum X coverage to calculate for coverage=T analysis 100
smrtscape minanchorx=X Minimum X coverage for anchor (preassembly error-correcting) subreads 6
smrtscape minreadlen=X Absolute minimum read length for calculations (use minlen=X to affect summary also) 500
smrtscape rqfilter=X Min read quality for filtered subreads 0.85
smrtscape rqstep=X Size of RQ jumps for calculation (min 0.001) 0.01
smrtscape smrtreads=X Average assemble output of a SMRT cell 50000
smrtscape smrtunits=X Units for smrtreads=X (reads/Gb/Mb) reads
smrtscape targetxcov=X Target 100% X Coverage for pre-assembly (e.g. error-corrected seed reads) 3
smrtscape xmargin=X "Safety margin" inflation of desired minimum X coverage 1
smrtscape xsteplen=X [Adv.] Size (bp) of increasing coverage steps for calculating required depths of coverage 1e5
smrtscape_V1 avread=X Average read length (bp) 20000
smrtscape_V1 errperbase=X Error-rate per base 0.14
smrtscape_V1 genomesize=X Genome size (bp) 0
smrtscape_V1 mapefficiency=X [Adv.] Efficiency of mapping anchor subreads onto seed reads for correction 1.0
smrtscape_V1 maxcov=X Maximum X coverage to calculate 100
smrtscape_V1 minanchorx=X Minimum X coverage for anchor subreads 6
smrtscape_V1 minreadlen=X Absolute minimum read length for calculations (use minlen=X to affect summary also) 500
smrtscape_V1 rqstep=X Size of RQ jumps for calculation (min 0.001) 0.01
smrtscape_V1 smrtreads=X Average assemble output of a SMRT cell 50000
smrtscape_V1 smrtunits=X Units for smrtreads=X (reads/Gb/Mb) reads
smrtscape_V1 targetcov=X Target percentage coverage for final genome 99.999
smrtscape_V1 targeterr=X Target errors per base for preassembly 1/genome size
smrtscape_V1 targetxcov=X Target 100% X Coverage for pre-assembly 3
smrtscape_V1 xmargin=X "Safety margin" inflation of X coverage 1
smrtscape_V1 xsteplen=X [Adv.] Size (bp) of increasing coverage steps for calculating required depths of coverage 1e5
snapper localmin=X Minimum length of local alignment to output to local stats table 10
snapper localsort=X Local hit field used to sort local alignments for localunique reduction Identity
snapper nocopylen=X Minimum length for CNV=0 fragments to be output 100
snapper nocopymerge=X CNV=0 fragments within X nt of each other will be merged prior to output 20
snapper spcode=X Overwrite species read from file (if any!) with X if generating sequence file from genbank None
snp_mapper spcode=X Overwrite species read from file (if any!) with X if generating sequence file from genbank None
spydarm backbase=X Prefix of backed up output files for previous release slimsuite.#DATE
spydarm basefile=X Prefix for output files slimsuite
spydarm prevbase=X Prefix of output files for previous release (to update) slimsuite
trex endbuffer=X Max distance from end of sequence to flag repeat for trimming 100
trex trimflank=X Additional flanking nucleotides to trim off the end of the sequence 200
trex trmode=X How to handle terminal tandem repeats (keep/trim/iterate) keep
unifake disdom=X Disorder threshold below which to annotate PFam domain as "DOMAIN" 0.0
unifake spcode=X Species code to use if it cannot be established from sequence name None

© 2015 RJ Edwards. Contact: richard.edwards@unsw.edu.au.