MAFFT_TG
runtime_ - Float - Maximum Hours to Run (click here for help setting this correctly)
infile_ - Primary Input File
all_outputfiles_ - Results -
outputfile_ - Results -
tree_outputfile_ - Results -
Section: ****************************************************************************
overall
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datatype_ - Excl - Input type
auto_analysis_ - Switch - Automatically select an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2 (based on data size) (--auto)
analysis_type_ - Excl - Use a preconfigured MAFFT strategy that:
configure_analysis_ - Switch - I want to configure my own analysis from scratch: (--mafft)
accurate_executable_ - Excl - Choose a MAFFT accurate executable
fast_executables_ - Excl - Choose a fast MAFFT executable
rna_executable_ - Excl - Choose a MAFFT RNA structure executable
use_contrafold_ - Switch - Use Contrafold rather than McCaskill algorithm (--contrafold)
xinsi_option_ - Excl - Which X-INS-i option should be used
Section: ****************************************************************************
para_algorithm
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distanceMetric_ - Excl - Distance metric
weighting_factor_ - Float - Weighting factor for the consistency term calculated from pairwise alignments (--weighti)
retrees_ - Integer - Number of times guide tree is built in progressive stage (--retree)
iterativeRefinements_ - Integer - Number of cycles of iterative refinement (-maxiterate)
useFFT_ - Excl - FFT approximation in group-to-group alignment
noScore_ - Excl - Check alignment score in iterative refinement stage ( --noscore)
memSave_ - Excl - Use the Myers-Miller (1988) algorithm (--memsave)
usePartTree_ - Excl - Use the PartTree algorithm for tree building.
partTreeMetric_ - Excl - PartTree distance metric
partTreePartitions_ - Integer - Number of partitions in the PartTree algorithm (--partsize)
maxAlignment_ - Integer - Maximum alignment size (--groupsize)
Section: ****************************************************************************
para_parameters
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use_seed_ - Switch - Use a Seed Alignment (--seed)
seed_alignment1_ - InFile - Select the Seed Alignment
use_add_ - Switch - Use Add Alignment (--add)
add_alignment1_ - InFile - Select the Alignment to add unaligned sequences to
use_addfrag_ - Switch - Use Addfragments Alignment (--addfragments)
large_align_ - Switch - Fast Alignment for Large data set (--6merpair)
ref_alignment1_ - InFile - Select the Reference Alignment
reorder_add_ - Switch - Reorder Output Alignment (--reorder)
use_addprof_ - Switch - Add Aligned Sequences to an Existing Alignment (--addprofile)
existing_alignment1_ - InFile - Select the Existing Alignment
use_merge_ - Switch - Merge Two or more sub-MSAs into a single file (--merge)
submsa_table_ - InFile - Select the SUBMSA Table
treein_tree_ - InFile - Provide a Guide Tree for Merge
Section: ****************************************************************************
para_parameters
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dnaMatrix_ - Excl - Nucleic Acid matrix selection (--kimura)
aaMatrix_ - Excl - Amino Acid matrix selection
jtt_ - Integer - JTT PAM matrix (Jones et al. 1992) selection (--jtt)
tm_ - Integer - Transmembrane PAM matrix (Jones et al. 1994) selection (--tm)
userMatrix_ - InFile - User-defined amino acid scoring matrix in BLAST format (--aamatrix)
opPenaltyGroupToGroup_ - Float - Gap opening penalty for group-to-group alignment (--op)
extendPenaltyGroupToGroup_ - Float - Offset value (gap extension penalty) for group-to-group alignment (--ep)
opPenaltyPairwise_ - Float - Gap open penalty for pairwise alignment (--lop)
offsetValuePairwise_ - Float - Offset value for pairwise alignment (--lep)
extendPenaltyPairwise_ - Float - Gap extension penalty for pairwise alignment (--lexp)
opPenaltySkip_ - Float - Gap open penalty for skipping the alignment (--LOP)
extendPenaltySkip_ - Float - Gap extension penalty for skipping the alignment (--LEXP)
fmodel_ - Excl - Incorporate AA/nucleotide composition information into the scoring matrix (--fmodel)
Section: ****************************************************************************
para_io
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outputFormat_ - Excl - Output format
outputOrder_ - Excl - Output order
outputGuideTree_ - Excl - Output guide tree (--treeout)