Seaview on Helix

Seaview is a graphical multiple sequence alignment editor. It is able to read and write various alignment formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows one to manually edit the alignment, and also to run DOT-PLOT or CLUSTALW/MUSCLE programs to locally improve the alignment.

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 staff@helix.nih.gov

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.

Helix Systems Scientific Supercomputing at the NIH