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Multiple sequence Alignment tool - Is there a tool? (Aug/04/2005 )

Does anyone know if there is any tool that offer to do Multiple sequence Alignment according to database name and Accession number, and not according the sequence. I have a large number of accessions that I want to align and it’s nearly impossible to get all the sequences and compare them.



Attached FileHi

Whether ur r trying to align protein sequences or nucleotide sequences.
There is no such option in clustalw or in clustalx.How many seq do u have?
any way. If iam not wrong

The following suggestion may be helpful u try it out


1 . if it is protein sequence u should ensure from which database ur getting it and moreover in "PIR" database ur search results will also contain a link for multiple sequence alignment where u can select the sequence and align .it works at online ( But the limitation is 50 seq).

2. if ur taking from "NCBI" what u have to do is select the sequence and click to display in FASTA format and ask to send the file to desktop. It takes only few seconds. u can view upto 500 seq in one page by clicking on sequences per page option and select all and save it.

By this way u can save the entire sequence in fasta format as a single file which u can use further for alignment.

in case if u want selected sequence from a list the only way is copying the sequence to the clipboard ( u can copy 500 seq ) and saving it as I mentioned above. After u have save follow the clipboard link above.

plz see attachment


1. the same way can be followed for nucleotide sequence.


1. The clustalw is only in online version and limit is 50
2. Clustalx u can download [ofline] but u need a single input file which u can make by the above said ways.
3. Either or both of the above u can use.
4. For treeview the tree only looks good if the seq r <50.
5. U can view unrooted tree well for even > 100 seq
6. use can also use Phylodraw better for seq bet 100 - 200

I hope the above works well . Best of luck
plz free to contact me at



A good help in microbial biodiversity is given by ARB where your sequences could be aligne with a big 16S dataset pre-aligned...BUT this software is off-line, not directly connected to internet and also is a little complicate (I forgot that is only for linux).
Another possibility is to use bioedit that is a alignemnt sequence editor software. this allows easily to align by Clustal the selected sequences and also is possible to performs blast searches directly rom the main windows, retrieve sequences (with all the GenBank information) directli from NCBI and align again... if well setted is also possible to use the complete phylip package to make trees.

I hope to be helpful for you