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 main UGENE User Manual.
Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| Gap extension penalty | Gap Extension Penalty. Positive values give rewards to gaps and prevent the alignment of unrelated segments. | 0 |
| Gap open penalty | Gap open penalty. Must be negative, best matches get a score of 1000. | -50 |
| Max iteration | Number of iteration on the progressive alignment. 0 - no iteration, -1 - Nseq iterations. | 0 |
| Tool path (required) | Path to the ClustalW tool. The default path can be set in the UGENE Application Settings. | default |
| Temporary directory | Directory to store temporary files. | default |
Parameters in Workflow File
Type: tcoffee
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| gap-ext-penalty | Offset | numeric |
| gap-open-penalty | Gap open penalty | numeric |
| iterations-max-num | Max iteration | numeric |
| path | Tool path | string |
| temp-dir | Temporary directory | 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 |