Align with T-Coffee Element
T-Coffee is a multiple sequence alignment package.
T-Coffee is used as an external tool from UGENE and it must be installed on your system. To learn more about the external tools, please read the main UGENE User Manual.
Element type: tcoffee
Parameters
| Parameter | Description | Default value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Gap extension penalty | Gap extension penalty. Positive values reward gaps and prevent the alignment of unrelated segments. | 0 | gap-ext-penalty | numeric |
| Gap open penalty | Gap open penalty. Must be negative, the best matches get a score of 1000. | -50 | gap-open-penalty | numeric |
| Max iteration | Number of iterations on the progressive alignment. 0 - no iteration, -1 - Nseq iterations. | 0 | iterations-max-num | numeric |
| Tool path (required) | Path to the ClustalW tool. The default path can be set in the UGENE Application Settings. | default | path | string |
| Temporary directory | Directory to store temporary files. | default | temp-dir | string |
Input/Output Ports
The element has 1 input port:
Name in GUI: Input MSA
Name in Workflow File: in-msa
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| MSA | msa | msa |
And 1 output port:
Name in GUI: Multiple sequence alignment
Name in Workflow File: out-msa
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| MSA | msa | msa |