SeWeR: Sequence Alignment

Select the program of choice.
Paste your query in the query box. Click Submit button to pass on the query with default options. Please note that some programs might have some options/parameters that are required. Also note that SeWeR doesn't check whether the required option(s)/parameter(s) is supplied or not. See program description for details.
Click Options button to fill up options. The button is a toggle. Clicking it again will close the option.
Click Customize to customize this search. Fill up all the options that you require, then click Customize. SeWeR will open another window with a customized page. Save that file on your computer.
Click Help to check the help page of the selected program. SeWeR will open a new window to show the help page.
Click Submit to pass on the query. SeWeR will open a new window for results.

Program Name

Your Email	Alignment Title	CPU Mode	Color Alignment
Output Format		Alignment	Output order
Fast Pairwise Alignment Options
KTUP (Word Size)	Window Length	Score Type	Pairgap	Topdiag
Multiple Sequence Alignment Options
Matrix	Gap Open	End Gaps	Gap Distances	Gap Extension
Phylogenetic Tree
Tree Type	Correct Distances			Ignore Gaps

ClustalW

At EBI server. Align multiple sequence. Input type, DNA or protein sequences. See help to find out the input format of the sequences. Required option, none.

Block Maker

At Fred Hutchinson Cancer Research Center. Finds conserved blocks in a group of two or more unaligned protein sequences. At least two protein sequences must be provided to make blocks. Each sequence must have a unique name of 10 characters or less. All sequences must be of same format (FASTA). Input type- protein sequences. Required option- email for 25 sequences or more than 15,000 amino acids.

HMMER

alistat - show statistics for a multiple alignment file. Input type: . Required options: email multali_file.

ComAlign

Combining many multiple alignments in one improved alignment. Input type: Sequences File (-f). Required options: email seq.

block maker
Your email	Sequence Description