Aligning with T-Coffee

Task Name: align-tcoffee

Create alignments with T-Coffee. T-Coffee is a collection of tools for computing, evaluating, and manipulating multiple alignments of DNA, RNA, and Protein sequences.

T-Coffee is used as an external tool and must be installed on your system.

Parameters:

  • gap-ext-penalty: Gap Extension Penalty. Positive values give rewards to gaps and prevent the alignment of unrelated segments (default is ‘0’) [Number]

  • gap-open-penalty: Gap Open Penalty. Must be negative; best matches get a score of 1000 (default is ‘-50’) [Number]

  • iter-max: Number of iterations on the progressive alignment: 0 - no iteration (default), -1 - Nseq iterations (default is ‘0’) [Number]

  • toolpath: T-Coffee location (default is the path specified in UGENE) [String]

  • tmpdir: Directory to store temporary files (default is UGENE temporary directory) [String]

  • in: Input alignment [URL datasets]

  • format: Document format of output alignment (default is ‘clustal’) [String]

  • out: Output alignment [String]

Example:

ugene align-tcoffee --in=test.aln --out=test_out.aln --format=clustal
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