Date: Thu, 28 Mar 2024 21:37:47 +0700 (NOVT) Message-ID: <1933729778.86894.1711636667025@ugene.net> Subject: Exported From Confluence MIME-Version: 1.0 Content-Type: multipart/related; boundary="----=_Part_86893_1385108481.1711636667024" ------=_Part_86893_1385108481.1711636667024 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Content-Location: file:///C:/exported.html
Originally, MAFFT is a multiple s= equence alignment program for unix-like operating systems. Currently, Windo= ws version is also available.
MAFFT is used as an external tool from UGENE and it must be instal= led on your system. To learn more about the external tools, please, read ma= in UGENE Use= r Manual.
MAFFT is use= d as an external tool from UGENE and it must be installed on your system. T= o learn more about the external tools, please, read main UGENE U= ser Manual.=
Parameter | Description | Default value |
---|---|---|
Offset | Works like gap extension penalty. | 0 |
Gap open penalty | Gap open penalty. | 1.53 |
Max iteration | Maximum number of iterative refinement. | 0 |
Tool path (default) | 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: mafft
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= span>
The element has 1 input port:
Name in GUI: Input MSA
Name in Workflow&nbs= p;File: in-msa
Slots:
Slot In GUI | Slot in Workflow File | Type |
---|---|---|
MSA | msa | msa |
And 1 <= /span>output port:
Name in GUI: Multiple sequence alignment
Name in Workflow&nbs= p;File: out-msa
Slots:
Slot In GUI | Slot in Workflow File | Type |
---|---|---|
MSA | msa | msa |