This interface is used from the REST API to convey input files, and configure the command line MAFFT parameters. .
The Tool ID for this interface is MAFFT_XSEDE. It is selected with toolId=MAFFT_XSEDE
The current version is 7.505
Supported parameters: Input files:
input.infile_ - Primary Input File
input.seed_alignment1_ - InFile - Select the Seed Alignment (when use_seed_=1)
input.add_alignment1_ - InFile - Select the Alignment to add unaligned sequences to use (when use_add_=1)
input. ref_alignment1_ - InFile - Select the Reference Alignment (use_addfrag_=1)
existing_alignment1_ - InFile - Select the Existing Alignment (use_addprof_=1)
input.submsa_table_ - InFile - Select the SUBMSA Table (use_merge_=1)
input. treein_tree_ - InFile - Provide a Guide Tree for Merge Section (use_merge_=1)
input.userMatrix_ - InFile - User-defined amino acid scoring matrix in BLAST format (--aamatrix) only if aaMatrix_=3
Supported parameters:
varam.runtime_ - Float - Maximum Hours to Run (0.5=default; 168 = maximum)
vparam.datatype_ - Excl - Input type; 0 (default)=determine automatically; dna; protein
vparam.anysymbol_ - Switch - adds --anysymbol for unusal characters. default=0
vparam.auto_analysis_ - Switch - Automatically select an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2 (based on data size) (--auto) default=1.
vparam.analysis_type_ - Excl - Use a preconfigured MAFFT strategy that: accurate (Favors accuracy, default); fast (Favors speed); rna (Considers RNA structure); protein (Considers protein structure)
vparam.configure_analysis_ - Switch - I want to configure my own analysis from scratch: (--mafft) default=0, vparam.auto_analysis must be 0
vparam.accurate_executable_ - Excl - Choose a MAFFT accurate executable; vparam.configure_analysis must=accurate; linsi68 (L-INS-i; default); ginsi68 (G-INS-i); einsi68 (E-INS-i); ftnsi (FFT-NS-i)
vparam.fast_executables_ - Excl - Choose a fast MAFFT; vparam.configure_analysis must=fast; fftnsi2 (FFT-NS-i; 2 cycles); fftnsi1000 (FFT-NS-i;1000 cycles); fftns168 (FFT-NS-1, 0 cycles); fftns268; (FFT-NS-2, 0 cycles); nwnsi68 (NW-NS-i, 2 cycles); nwns268 (NW-NS-2); nwns268part (NW-NS-PartTree)
vparam.executable rna_executable_ - Excl - Choose a MAFFT RNA structure executable; vparam.configure_analysis must=rna; qinsi (Q-INS-i, default); xinsi (X-INS-i)
vpara,use_contrafold_ - Switch - Use Contrafold rather than McCaskill algorithm (--contrafold) default=0
vparam.xinsi_option_ - Excl - Which X-INS-i option should be used ? larapair (deault); foldalignlocalpair; foldalignglobalpair; scarnapair (MXSCARNA)
Algoorithm Option
vparam.distanceMetric_ - Excl - Distance metric: 0 (6merpair, default); 1 (globalpair); 2 (localpair); 3 (genafpair); 4 (fastapair)
vparam.weighting_factor_ - Float -Weighting factor for the consistency term calculated from pairwise alignments (--weighti) default=2.7
vparam.retrees_ - Integer - Number of times guide tree is built in progressive stage (--retree) default=2
vparam.iterativeRefinements_ - Integer - Number of cycles of iterative refinement (-maxiterate) default=0
vparam.useFFT_ - Excl - FFT approximation in group-to-group alignment 0=off; 1=on; default=1
vparam.noScore_ - Excl - Check alignment score in iterative refinement stage ( --noscore) 0=no; 1=yes; default=1
vparam.memSave_ - Excl - Use the Myers-Miller (1988) algorithm (--memsave) 0=auto-select; 1=yes; default=0
vparam.usePartTree_ - Excl - Use the PartTree algorithm for tree building. 0=no; 1=yes; default=no
vparam.partTreeMetric_ - Excl - PartTree distance metric; 0 (6-mer, default); 1 (DP); 2 (FASTA)
vparam.partTreePartitions_ - Integer - Number of partitions in the PartTree algorithm (--partsize) default=50
vparam.maxAlignment_ - Integer - Maximum alignment size (--groupsize) Section: vparam.usePartTree must = 1
vparam.adjust_direction_ - Switch - adjust the direction of nucleotide sequences, according to the first sequence (6mer based) default = 0
vparam.accuratelyadjust_direction - Switch - adjust the direction of highly diverged nucleotide sequences, according to the first sequence (DP based, slow) default=0
Seed/Profile/Merge Options
vparam.use_seed_ - Switch - Use a Seed Alignment (--seed) default=0
vparam.use_add_ - Switch - Use Add Alignment (--add) default=0< br /> vparam.addfrag_ - Switch - Use Addfragments Alignment (--addfragments) default=0
vparam.large_align_ - Switch - Fast Alignment for Large data set (--6merpair) default=0
vparam.reorder_add_ - Switch - Reorder Output Alignment (--reorder) default=0
vparam.keeplength_ - Switch - Preserve Alignment length while adding sequences (--keeplength)
vparam.usemapout_ - Switch - See a correspondence table of positions after adding (--mapout)
vparam.use_addprof_ - Switcusemapouth - Add Aligned Sequences to an Existing Alignment (--addprofile) default=0
vparam.use_merge_ - Switch - Merge Two or more sub-MSAs into a single file (--merge) default=0
Algorithm Parameters
vparam.dnaMatrix_ - Excl - Nucleic Acid matrix selection (--kimura) 200 (200PAM/kappa=2, default); 20 (20PAM / kappa=2); 1 (1PAM / kappa=2)
vparam.aaMatrix_ - Excl - Amino Acid matrix selection: 0 (BLOSUM (Henikoff and Henikoff 1992); 1 (JTT PAM Jones et al. 1992; 2 (Transmembrane PAM Jones et al. 1994); 3 (User-defined)
vparam.jtt_ - Integer - JTT PAM matrix (Jones et al. 1992) selection (--jtt)
vparam.tm_ - Integer - Transmembrane PAM matrix (Jones et al. 1994) selection (--tm) )
vparam.opPenaltyGroupToGroup_ - Float - Gap opening penalty for group-to-group alignment (--op) default=1.53
vparam.extendPenaltyGroupToGroup_ - Float - Offset value (gap extension penalty) for group-to-group alignment (--ep) default=0.123
vparam.opPenaltyPairwise_ - Float - Gap open penalty for pairwise alignment (--lop) default=-2.00
vparam.offsetValuePairwise_ - Float - Offset value for pairwise alignment (--lep) default=0.1
vparam.extendPenaltyPairwise_ - Float - Gap extension penalty for pairwise alignment (--lexp) default=-0.1
vparam.opPenaltySkip_ - Float - Gap open penalty for skipping the alignment (--LOP) defalkt=-6.00
vparam.extendPenaltySkip_ - Float - Gap extension penalty for skipping the alignment (--LEXP) default=0.00
vparam.fmodel_ - Excl - Incorporate AA/nucleotide composition information into the scoring matrix (--fmodel) 0=no; 1=yes; default=0
Output Parameters
vparam.outputFormat_ - Excl - Output format; 0=FASTA; 1=Custal; default=0
vparam.outputOrder_ - Excl - Output order; 0=input order; 1=reorderl; default=0
vparam.outputGuideTree_ - Excl - Output guide tree (--treeout) 0=no; 1=yes; default=no
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