Task Name: align-clustalo
Create alignment with ClustalO. ClustalO is a general purpose multiple sequence alignment program for proteins.
ClustalO is used as an external tool and must be installed on your system.
Parameters:
in - Input alignment [Url datasets]
format - Document format of output alignment (using 'clustal' by default) [String]
out - Output alignment [String]
max-guidetree-iterations - Maximum number guidetree iterations (using '0' by default) [Number]
max-hmm-iterations - Maximum number of HMM iterations (using '0' by default) [Number]
iter - Number of (combined guide-tree/HMM) iterations (using '1' by default) [Number]
toolpath - ClustalO location (using the path specified in UGENE by default) [String]
auto - Set options automatically (might overwrite some of your options) (using 'False' by default) [Boolean]
tmpdir - Directory to store temporary files (using UGENE temporary directory by default) [String]
Example:
ugene align-clustalw --in=test.aln --out=test_out.aln --format=clustal