Seaview was developed by Manolo Gouy at CNRS, France. Seaview for Macs and PCs is available for download from the Seaview website
Seaview can be used to edit/view files or alignments produced by Emboss, ClustalW or GCG. Files in GCG's proprietary RSF format should be converted to MSF format using the ClustalW program, as described below. If you have a large number of old GCG RSF files and cannot easily convert them, You can request the Helix staff for help by sending email to firstname.lastname@example.org
To access sequence files or alignments produced by ClustalW or Emboss on Helix, an Xwindows connection to Helix is required.
Sample session for converting a GCG RSF file into MSF using ClustalW: (user input in bold)
<helix>54% clustalw -INFILE=polycys.rsf -outfile=polycys.msf -convert CLUSTAL W (1.81) Multiple Sequence Alignments Sequence format is RSF Sequence 1: 14781151 684 aa Sequence 2: 14781149 684 aa Sequence 3: af182034 684 aa Sequence 4: np_055201 684 aa Sequence 5: np_058623 684 aa [...] Sequence 40: np_035836 696 aa Sequence 41: np_58904 694 aa Sequence 42: np_35837 694 aa CLUSTAL-Alignment file created [polycys.msf] <helix>55%
To run Seaview, make an Xwindows connection to Helix, and type 'seaview' or 'seaview myfile.msf' at the prompt. Screenshots from Seaview:
Tips: To display a consensus sequence, select the desired sequences by clicking on their names. Then click on the 'Edit' pulldown menu, and select 'Consensus sequence'.
To create a postscript output file, go to the 'File' menu, then 'prepare PS'. In the resulting popup window, enter the name for your Postscript file. Sample Postscript file output from Seaview.