Child pages
  • Aligning with T-Coffee
Skip to end of metadata
Go to start of metadata

You are viewing an old version of this page. View the current version.

Compare with Current View Page History

Version 1 Current »

Task Name: align-tcoffee

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

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


gap-ext-penalty - Gap Extension Penalty. Positive values give rewards to gaps and prevent the alignment of unrelated segments (using '0' by default) [Number]

gap-open-penalty - Gap Open Penalty. Must be negative, best matches get a score of 1000 (using '-50' by default) [Number]

iter-max - Number of iteration on the progressive alignment: 0 - no iteration (default), -1 - Nseq iterations (using '0' by default) [Number]

toolpath - T-Coffee location (using the path specified in UGENE by default) [String]

tmpdir - Directory to store temporary files (using UGENE temporary directory by default) [String]

in - Input alignment [Url datasets]

format - Document format of output alignment (using 'clustal' by default) [String]

out - Output alignment [String]


ugene align-tcoffee  --in=test.aln --out=test_out.aln --format=clustal
  • No labels