T-Coffee is a multiple sequence alignment package.
| Warning |
|---|
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 |