exonerate -h
** (process:121002): WARNING **: 21:41:53.839: Compiled with assertion checking - will run slowly
exonerate from exonerate version 2.4.0
Using glib version 2.42.2
Built on Mar 24 2016
exonerate: A generic sequence comparison tool
Guy St.C. Slater. guy@ebi.ac.uk. 2000-2009.
Examples of use:
1. Ungapped alignment of any DNA or protein sequences:
exonerate queries.fa targets.fa
2. Gapped alignment of Mouse proteins to Fugu proteins:
exonerate --model affine:local mouse.fa fugu.fa
3. Find top 10 matches of each EST to a genome:
exonerate --model est2genome --bestn 10 est.fa genome.fa
4. Find proteins with at least a 50% match to a genome:
exonerate --model protein2genome --percent 50 p.fa g.fa
5. Perform a full Smith-Waterman-Gotoh alignment:
exonerate --model affine:local --exhaustive yes a.fa b.fa
6. Many more combinations are possible. To find out more:
exonerate --help
man exonerate
General Options:
---------------
-h --shorthelp [FALSE] <TRUE>
--help [FALSE]
-v --version [FALSE]
Sequence Input Options:
----------------------
-q --query [mandatory] <*** empty list ***>
-t --target [mandatory] <*** empty list ***>
-Q --querytype [unknown]
-T --targettype [unknown]
--querychunkid [0]
--targetchunkid [0]
--querychunktotal [0]
--targetchunktotal [0]
-V --verbose [1]
Translation Options:
-------------------
--geneticcode [1]
Analysis Options:
----------------
-E --exhaustive [FALSE]
-B --bigseq [FALSE]
-r --revcomp [TRUE]
--forcescan [none]
--saturatethreshold [0]
--customserver [NULL]
-c --cores [1]
Fasta Database Options:
----------------------
--fastasuffix [.fa]
Gapped Alignment Options:
------------------------
-m --model [ungapped]
-s --score [100]
--percent [0.0]
--showalignment [TRUE]
--showsugar [FALSE]
--showcigar [FALSE]
--showvulgar [TRUE]
--showquerygff [FALSE]
--showtargetgff [FALSE]
--ryo [NULL]
-n --bestn [0]
-S --subopt [TRUE]
-g --gappedextension [TRUE]
--refine [none]
--refineboundary [32]
Viterbi algorithm options:
-------------------------
-D --dpmemory [32]
Code generation options:
-----------------------
-C --compiled [TRUE]
Heuristic Options:
-----------------
--terminalrangeint [12]
--terminalrangeext [12]
--joinrangeint [12]
--joinrangeext [12]
--spanrangeint [12]
--spanrangeext [12]
Seeded Dynamic Programming options:
----------------------------------
-x --extensionthreshold [50]
--singlepass [TRUE]
BSDP algorithm options:
----------------------
--joinfilter [0]
Sequence Options:
----------------
-A --annotation [none]
Symbol Comparison Options:
-------------------------
--softmaskquery [FALSE]
--softmasktarget [FALSE]
-d --dnasubmat [nucleic]
-p --proteinsubmat [blosum62]
Alignment Seeding Options:
-------------------------
-M --fsmmemory [256]
--forcefsm [none]
--wordjump [1]
--wordambiguity [1]
Affine Model Options:
--------------------
-o --gapopen [-12]
-e --gapextend [-4]
--codongapopen [-18]
--codongapextend [-8]
NER Model Options:
-----------------
--minner [10]
--maxner [50000]
--neropen [-20]
Intron Modelling Options:
------------------------
--minintron [30]
--maxintron [200000]
-i --intronpenalty [-30]
Frameshift Options:
------------------
-f --frameshift [-28]
Alphabet Options:
----------------
--useaatla [TRUE]
HSP creation options:
--------------------
--hspfilter [0]
--useworddropoff [TRUE]
--seedrepeat [1]
--dnawordlen [12]
--proteinwordlen [6]
--codonwordlen [12]
--dnahspdropoff [30]
--proteinhspdropoff [20]
--codonhspdropoff [40]
--dnahspthreshold [75]
--proteinhspthreshold [30]
--codonhspthreshold [50]
--dnawordlimit [0]
--proteinwordlimit [4]
--codonwordlimit [4]
--geneseed [0]
--geneseedrepeat [3]
Alignment options:
-----------------
--alignmentwidth [80]
--forwardcoordinates [TRUE]
SAR Options:
-----------
--quality [0]
Splice Site Prediction Options:
------------------------------
--splice3 [primate]
--splice5 [primate]
--forcegtag [FALSE]
--
exonerate --help
** (process:121224): WARNING **: 21:45:39.272: Compiled with assertion checking - will run slowly
exonerate from exonerate version 2.4.0
Using glib version 2.42.2
Built on Mar 24 2016
exonerate: A generic sequence comparison tool
Guy St.C. Slater. guy@ebi.ac.uk. 2000-2009.
Examples of use:
1. Ungapped alignment of any DNA or protein sequences:
exonerate queries.fa targets.fa
2. Gapped alignment of Mouse proteins to Fugu proteins:
exonerate --model affine:local mouse.fa fugu.fa
3. Find top 10 matches of each EST to a genome:
exonerate --model est2genome --bestn 10 est.fa genome.fa
4. Find proteins with at least a 50% match to a genome:
exonerate --model protein2genome --percent 50 p.fa g.fa
5. Perform a full Smith-Waterman-Gotoh alignment:
exonerate --model affine:local --exhaustive yes a.fa b.fa
6. Many more combinations are possible. To find out more:
exonerate --help
man exonerate
General Options:
---------------
-h --shorthelp
Display compact help text
Environment variable: $EXONERATE_EXONERATE_SHORTHELP (Not set)
Default: "FALSE"
--help
Displays verbose help text
Environment variable: $EXONERATE_EXONERATE_HELP (Not set)
Default: "FALSE"
Using: <TRUE>
-v --version
Show version number for this program
Environment variable: $EXONERATE_EXONERATE_VERSION (Not set)
Default: "FALSE"
Sequence Input Options:
----------------------
-q --query <path>
Specify query sequences as a fasta format file
Environment variable: $EXONERATE_EXONERATE_QUERY (Not set)
*** This argument is mandatory ***
<*** empty list ***>
-t --target <path>
Specify target sequences as a fasta format file
Environment variable: $EXONERATE_EXONERATE_TARGET (Not set)
*** This argument is mandatory ***
<*** empty list ***>
-Q --querytype <alphabet type>
Specify query alphabet type
Environment variable: $EXONERATE_EXONERATE_QUERYTYPE (Not set)
Default: "unknown"
-T --targettype <alphabet type>
Specify target alphabet type
Environment variable: $EXONERATE_EXONERATE_TARGETTYPE (Not set)
Default: "unknown"
--querychunkid
Specify query job number
Environment variable: $EXONERATE_EXONERATE_QUERYCHUNKID (Not set)
Default: "0"
--targetchunkid
Specify target job number
Environment variable: $EXONERATE_EXONERATE_TARGETCHUNKID (Not set)
Default: "0"
--querychunktotal
Specify total number of query jobs
Environment variable: $EXONERATE_EXONERATE_QUERYCHUNKTOTAL (Not set)
Default: "0"
--targetchunktotal
Specify total number of target jobs
Environment variable: $EXONERATE_EXONERATE_TARGETCHUNKTOTAL (Not set)
Default: "0"
-V --verbose <level>
Show search progress
Environment variable: $EXONERATE_EXONERATE_VERBOSE (Not set)
Default: "1"
Translation Options:
-------------------
--geneticcode
Use built-in or custom genetic code
Environment variable: $EXONERATE_EXONERATE_GENETICCODE (Not set)
Default: "1"
Analysis Options:
----------------
-E --exhaustive
Perform exhaustive alignment (slow)
Environment variable: $EXONERATE_EXONERATE_EXHAUSTIVE (Not set)
Default: "FALSE"
-B --bigseq
Allow rapid comparison between big sequences
Environment variable: $EXONERATE_EXONERATE_BIGSEQ (Not set)
Default: "FALSE"
-r --revcomp
Also search reverse complement of query and target
Environment variable: $EXONERATE_EXONERATE_REVCOMP (Not set)
Default: "TRUE"
--forcescan <[q|t]>
Force FSM scan on query or target sequences
Environment variable: $EXONERATE_EXONERATE_FORCESCAN (Not set)
Default: "none"
--saturatethreshold <int>
Word saturation threshold
Environment variable: $EXONERATE_EXONERATE_SATURATETHRESHOLD (Not set)
Default: "0"
--customserver <command>
Custom command to send non-standard server
Environment variable: $EXONERATE_EXONERATE_CUSTOMSERVER (Not set)
Default: "NULL"
-c --cores <number>
Number of cores/CPUs/threads for alignment computation
Environment variable: $EXONERATE_EXONERATE_CORES (Not set)
Default: "1"
Fasta Database Options:
----------------------
--fastasuffix <suffix>
Fasta file suffix filter (in subdirectories)
Environment variable: $EXONERATE_EXONERATE_FASTASUFFIX (Not set)
Default: ".fa"
Gapped Alignment Options:
------------------------
-m --model <alignment model>
Specify alignment model type
Supported types:
ungapped ungapped:trans
affine:global affine:bestfit affine:local affine:overlap
est2genome ner protein2dna protein2genome
protein2dna:bestfit protein2genome:bestfit
coding2coding coding2genome cdna2genome genome2genome
Environment variable: $EXONERATE_EXONERATE_MODEL (Not set)
Default: "ungapped"
-s --score <threshold>
Score threshold for gapped alignment
Environment variable: $EXONERATE_EXONERATE_SCORE (Not set)
Default: "100"
--percent <threshold>
Percent self-score threshold
Environment variable: $EXONERATE_EXONERATE_PERCENT (Not set)
Default: "0.0"
--showalignment
Include (human readable) alignment in results
Environment variable: $EXONERATE_EXONERATE_SHOWALIGNMENT (Not set)
Default: "TRUE"
--showsugar
Include 'sugar' format output in results
Environment variable: $EXONERATE_EXONERATE_SHOWSUGAR (Not set)
Default: "FALSE"
--showcigar
Include 'cigar' format output in results
Environment variable: $EXONERATE_EXONERATE_SHOWCIGAR (Not set)
Default: "FALSE"
--showvulgar
Include 'vulgar' format output in results
Environment variable: $EXONERATE_EXONERATE_SHOWVULGAR (Not set)
Default: "TRUE"
--showquerygff
Include GFF output on query in results
Environment variable: $EXONERATE_EXONERATE_SHOWQUERYGFF (Not set)
Default: "FALSE"
--showtargetgff
Include GFF output on target in results
Environment variable: $EXONERATE_EXONERATE_SHOWTARGETGFF (Not set)
Default: "FALSE"
--ryo <format>
Roll-your-own printf-esque output format
Environment variable: $EXONERATE_EXONERATE_RYO (Not set)
Default: "NULL"
-n --bestn <number>
Report best N results per query
Environment variable: $EXONERATE_EXONERATE_BESTN (Not set)
Default: "0"
-S --subopt
Search for suboptimal alignments
Environment variable: $EXONERATE_EXONERATE_SUBOPT (Not set)
Default: "TRUE"
-g --gappedextension
Use gapped extension (default is SDP)
Environment variable: $EXONERATE_EXONERATE_GAPPEDEXTENSION (Not set)
Default: "TRUE"
--refine
Alignment refinement strategy [none|full|region]
Environment variable: $EXONERATE_EXONERATE_REFINE (Not set)
Default: "none"
--refineboundary
Refinement region boundary
Environment variable: $EXONERATE_EXONERATE_REFINEBOUNDARY (Not set)
Default: "32"
Viterbi algorithm options:
-------------------------
-D --dpmemory <Mb>
Maximum memory to use for DP tracebacks (Mb)
Environment variable: $EXONERATE_EXONERATE_DPMEMORY (Not set)
Default: "32"
Code generation options:
-----------------------
-C --compiled
Use compiled viterbi implementations
Environment variable: $EXONERATE_EXONERATE_COMPILED (Not set)
Default: "TRUE"
Heuristic Options:
-----------------
--terminalrangeint
Internal terminal range
Environment variable: $EXONERATE_EXONERATE_TERMINALRANGEINT (Not set)
Default: "12"
--terminalrangeext
External terminal range
Environment variable: $EXONERATE_EXONERATE_TERMINALRANGEEXT (Not set)
Default: "12"
--joinrangeint
Internal join range
Environment variable: $EXONERATE_EXONERATE_JOINRANGEINT (Not set)
Default: "12"
--joinrangeext
External join range
Environment variable: $EXONERATE_EXONERATE_JOINRANGEEXT (Not set)
Default: "12"
--spanrangeint
Internal span range
Environment variable: $EXONERATE_EXONERATE_SPANRANGEINT (Not set)
Default: "12"
--spanrangeext
External span range
Environment variable: $EXONERATE_EXONERATE_SPANRANGEEXT (Not set)
Default: "12"
Seeded Dynamic Programming options:
----------------------------------
-x --extensionthreshold
Gapped extension threshold
Environment variable: $EXONERATE_EXONERATE_EXTENSIONTHRESHOLD (Not set)
Default: "50"
--singlepass
Generate suboptimal alignment in a single pass
Environment variable: $EXONERATE_EXONERATE_SINGLEPASS (Not set)
Default: "TRUE"
BSDP algorithm options:
----------------------
--joinfilter
BSDP join filter threshold
Environment variable: $EXONERATE_EXONERATE_JOINFILTER (Not set)
Default: "0"
Sequence Options:
----------------
-A --annotation <path>
Path to sequence annotation file
Environment variable: $EXONERATE_EXONERATE_ANNOTATION (Not set)
Default: "none"
Symbol Comparison Options:
-------------------------
--softmaskquery
Allow softmasking on the query sequence
Environment variable: $EXONERATE_EXONERATE_SOFTMASKQUERY (Not set)
Default: "FALSE"
--softmasktarget
Allow softmasking on the target sequence
Environment variable: $EXONERATE_EXONERATE_SOFTMASKTARGET (Not set)
Default: "FALSE"
-d --dnasubmat <name>
DNA substitution matrix
Environment variable: $EXONERATE_EXONERATE_DNASUBMAT (Not set)
Default: "nucleic"
-p --proteinsubmat <name>
Protein substitution matrix
Environment variable: $EXONERATE_EXONERATE_PROTEINSUBMAT (Not set)
Default: "blosum62"
Alignment Seeding Options:
-------------------------
-M --fsmmemory <Mb>
Memory limit for FSM scanning
Environment variable: $EXONERATE_EXONERATE_FSMMEMORY (Not set)
Default: "256"
--forcefsm <fsm type>
Force FSM type ( normal | compact )
Environment variable: $EXONERATE_EXONERATE_FORCEFSM (Not set)
Default: "none"
--wordjump
Jump between query words
Environment variable: $EXONERATE_EXONERATE_WORDJUMP (Not set)
Default: "1"
--wordambiguity
Number of ambiguous words to expand
Environment variable: $EXONERATE_EXONERATE_WORDAMBIGUITY (Not set)
Default: "1"
Affine Model Options:
--------------------
-o --gapopen <penalty>
Affine gap open penalty
Environment variable: $EXONERATE_EXONERATE_GAPOPEN (Not set)
Default: "-12"
-e --gapextend <penalty>
Affine gap extend penalty
Environment variable: $EXONERATE_EXONERATE_GAPEXTEND (Not set)
Default: "-4"
--codongapopen <penalty>
Codon affine gap open penalty
Environment variable: $EXONERATE_EXONERATE_CODONGAPOPEN (Not set)
Default: "-18"
--codongapextend <penalty>
Codon affine gap extend penalty
Environment variable: $EXONERATE_EXONERATE_CODONGAPEXTEND (Not set)
Default: "-8"
NER Model Options:
-----------------
--minner <length>
Minimum NER length
Environment variable: $EXONERATE_EXONERATE_MINNER (Not set)
Default: "10"
--maxner <length>
Maximum NER length
Environment variable: $EXONERATE_EXONERATE_MAXNER (Not set)
Default: "50000"
--neropen <score>
NER open penalty
Environment variable: $EXONERATE_EXONERATE_NEROPEN (Not set)
Default: "-20"
Intron Modelling Options:
------------------------
--minintron <length>
Minimum intron length
Environment variable: $EXONERATE_EXONERATE_MININTRON (Not set)
Default: "30"
--maxintron <length>
Maximum intron length
Environment variable: $EXONERATE_EXONERATE_MAXINTRON (Not set)
Default: "200000"
-i --intronpenalty <score>
Intron Opening penalty
Environment variable: $EXONERATE_EXONERATE_INTRONPENALTY (Not set)
Default: "-30"
Frameshift Options:
------------------
-f --frameshift <penalty>
Frameshift creation penalty
Environment variable: $EXONERATE_EXONERATE_FRAMESHIFT (Not set)
Default: "-28"
Alphabet Options:
----------------
--useaatla
Use three-letter abbreviation for AA names
Environment variable: $EXONERATE_EXONERATE_USEAATLA (Not set)
Default: "TRUE"
HSP creation options:
--------------------
--hspfilter
Aggressive HSP filtering level
Environment variable: $EXONERATE_EXONERATE_HSPFILTER (Not set)
Default: "0"
--useworddropoff
Use word neighbourhood dropoff
Environment variable: $EXONERATE_EXONERATE_USEWORDDROPOFF (Not set)
Default: "TRUE"
--seedrepeat
Seeds per diagonal required for HSP seeding
Environment variable: $EXONERATE_EXONERATE_SEEDREPEAT (Not set)
Default: "1"
--dnawordlen <bp>
Wordlength for DNA words
Environment variable: $EXONERATE_EXONERATE_DNAWORDLEN (Not set)
Default: "12"
--proteinwordlen <aa>
Wordlength for protein words
Environment variable: $EXONERATE_EXONERATE_PROTEINWORDLEN (Not set)
Default: "6"
--codonwordlen <bp>
Wordlength for codon words
Environment variable: $EXONERATE_EXONERATE_CODONWORDLEN (Not set)
Default: "12"
--dnahspdropoff <score>
DNA HSP dropoff score
Environment variable: $EXONERATE_EXONERATE_DNAHSPDROPOFF (Not set)
Default: "30"
--proteinhspdropoff <score>
Protein HSP dropoff score
Environment variable: $EXONERATE_EXONERATE_PROTEINHSPDROPOFF (Not set)
Default: "20"
--codonhspdropoff <score>
Codon HSP dropoff score
Environment variable: $EXONERATE_EXONERATE_CODONHSPDROPOFF (Not set)
Default: "40"
--dnahspthreshold <score>
DNA HSP threshold score
Environment variable: $EXONERATE_EXONERATE_DNAHSPTHRESHOLD (Not set)
Default: "75"
--proteinhspthreshold <score>
Protein HSP threshold score
Environment variable: $EXONERATE_EXONERATE_PROTEINHSPTHRESHOLD (Not set)
Default: "30"
--codonhspthreshold <score>
Codon HSP threshold score
Environment variable: $EXONERATE_EXONERATE_CODONHSPTHRESHOLD (Not set)
Default: "50"
--dnawordlimit <score>
Score limit for dna word neighbourhood
Environment variable: $EXONERATE_EXONERATE_DNAWORDLIMIT (Not set)
Default: "0"
--proteinwordlimit <score>
Score limit for protein word neighbourhood
Environment variable: $EXONERATE_EXONERATE_PROTEINWORDLIMIT (Not set)
Default: "4"
--codonwordlimit <score>
Score limit for codon word neighbourhood
Environment variable: $EXONERATE_EXONERATE_CODONWORDLIMIT (Not set)
Default: "4"
--geneseed <threshold>
Geneseed Threshold
Environment variable: $EXONERATE_EXONERATE_GENESEED (Not set)
Default: "0"
--geneseedrepeat <number>
Seeds per diagonal required for geneseed HSP seeding
Environment variable: $EXONERATE_EXONERATE_GENESEEDREPEAT (Not set)
Default: "3"
Alignment options:
-----------------
--alignmentwidth
Alignment display width
Environment variable: $EXONERATE_EXONERATE_ALIGNMENTWIDTH (Not set)
Default: "80"
--forwardcoordinates
Report all coordinates on the forward strand
Environment variable: $EXONERATE_EXONERATE_FORWARDCOORDINATES (Not set)
Default: "TRUE"
SAR Options:
-----------
--quality <percent>
HSP quality threshold
Environment variable: $EXONERATE_EXONERATE_QUALITY (Not set)
Default: "0"
Splice Site Prediction Options:
------------------------------
--splice3
Supply frequency matrix for 3' splice sites
Environment variable: $EXONERATE_EXONERATE_SPLICE3 (Not set)
Default: "primate"
--splice5
Supply frequency matrix for 5' splice sites
Environment variable: $EXONERATE_EXONERATE_SPLICE5 (Not set)
Default: "primate"
--forcegtag
Force use of gt...ag splice sites
Environment variable: $EXONERATE_EXONERATE_FORCEGTAG (Not set)
Default: "FALSE"
--
