Muscle5 Parallel REST

Muscle5 - Parallel

MUSCLE is widely-used software for making multiple alignments of biological sequences. Unlike Muscle 3.x, this version can run in parallel, and is far more scalable.

Version 5 of MUSCLE achieves highest scores on Balibase, Bralibase and Balifam benchmark tests and scales to thousands of sequences on a commodity desktop computer.

This version supports generating an ensemble of alternative alignments with the same high accuracy obtained with default parameters. By comparing downstream predictions from different alignments, such as trees, a biologist can evaluation the robustness of conclusions against alignment errors.

If you use Muscle5, please cite: R.C. Edgar (2021) "MUSCLE v5 enables improved estimates of phylogenetic tree confidence by ensemble bootstrapping"

Muscle 5 Manual

The Tool ID for this interface is tool=EPA_NG_XSEDE

Supported parameters:

input.infile_type1_= Tree file in Newick format
input.ref_upload_ = Specify a reference alignment; required for letterconf

vparam.runtime_= - Float - Maximum Hours to Run (up to 168 hours) (default=1.0)
vparam.select_inputtype_ = Excl - I want to: Allowed values: (align, explode, e2efa, resample, efastats, disperse, maxc, letterconf, columnconf) default = align; See the manual if you need help choosing
vparam.select_algorithm_ = Excl - Select the algorithm to use (only for aligning) align (defalt) or super5
vparam.specify_output_ = String - Specify an output name (required for alignments)
vparam.specify_prefix_ = String - specify a prefix, required for the explode command.
vparam.specify_suffix_ = Specify a suffix required for the explode command.
vparam.more_memory_ - Switch - I need more memory; only for alignments.

Align/Super5 Options
vparam.specify_seed_ - Integer - Random number seed for generating HMM perturbations (-perturb)
vparam.specify_perm_ - Excl - Specify the guide tree permutation (-perm) only for alignments. abc, acb, bca, all no default.
vparam.specify_consiters_ - Integer - Specify the number of consistency iterations (-consiters); alignments only.
vparam.specify_refineiters_ - Integer - Specify the number of refinement iterations (-refiniters) alignments only.
vparam.specify_datatype_ - Excl - Select the data type 1=auto-detect; 2=nucleotide; 3=amino acid; no default

Align Options
vparam.make_stratified_ - Switch - Make a stratified ensemble (-stratified)
vparam.make_diversified_ - Swtich - Make a diversified ensmble (-diversified); not with -perturb.
vparam.specify_alignreplicates_ - Integer - Specify the number of replicates (-replicates)
vparam.measure_dispersion_ - Measure dispersion of the ensemble (-disperse)

Replicates
vparam.specify_replicates_ -Integer - Specify the number of resample replicates (-replicates) Between 0 and 100.
vparam.specify_minconf_ - Float - Minimum column confidence (-minconf) between 0 and 1
vparam.specify_gapfrac_ - Float - Maximum fraction of gapped positions in a column (-gapfract) between 0 and 1

Confidence Calculations
vparam.use_html_ - Switch- Make an html output file (-html)
vparam.use_jalview_ - Switch - Create a jalview features file (-jalview)

 

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