Did you label the sequences (FASTA FORMAT) with different names ?

Hi,

I use Geneious R6, "Map" function. That allow to align against a user identified reference.

good luck

chandima 

There are only a few high quality aligners out there:

Muscle (as mentioned)

Mafft (http://mafft.cbrc.jp/alignment/server/)

and my favorite, Clustal Omega (http://www.ebi.ac.uk/Tools/msa/clustalo/)

ClustalW is old and is not in the same league with these other three.  However, you should not be getting an error when running it.  As mentioned make sure that you have unique names for each sequence.  If you try one of these server based approaches it should tell you what is wrong with your input after you submit.

you can try MEGA software for multi Fasta format sequences and align them with Muscle on default or you can set the parameters according to choice.

You can try the following tools

http://www.ibi.vu.nl/programs/veralignwww/

http://bioinfolab.unl.edu/~canderson/SuiteMSA/

Multiple alignment tools will always try to align all sequences you give as an input. If some spot is more similar between some of them ALL other sequences will unavoidably be "pulled" to this spot. So if you think there are sequences in your set that should map to DIFFERENT regions on your plasmid sequence, you should not use standard multiple alignmemt tools (any). As a solution (quite "lazy", as you requested:)) I would suggest you to have a look at pairwise alignments that are anyway produced by Clustal (in the on-line version they are shown, in the locally installed version not). This will give you the idea of which sequences can be aligned together (probably there will be several groups). Otherwise, I'd suggest Lagan Vista, play around, there are several options and it gives also pairwise plots.

I agree with Harlan, MAFFT is a great multiple sequence alignment program. You can run it via the web server or download it and run it locally.

I also think that looking at some pairwise alignments will help you determine which one's can be aligned well together and which are going to cause some issues for you.

I'll second the notion to try MEGA, using muscle. For anyone getting started with alignments, that's a great tool to tinker with

http://www.megasoftware.net/

I know this question is several years old, but I'll add my two cents in case it helps anyone else. I'm unfamiliar with the tools above, but I'm looking to do something similar with genomic sequencing vs. a reference file so I'll be checking them out. For plasmid sequences, I really like A Plasmid Editor (ApE). It's free and the multiple alignment is extremely easy to use; just open your sequence files in the program and set your reference (even select a subset of that sequence for alignment) and let it either pick the best direction or force it to align forward or reverse. The really nice part is that if you've used the features function to label and annotate your plasmid, you can see those features on your alignment. It's a great little program for simpler projects like comparing clones from bacterial transformation.

Hi! Alanna Roff . Currently I want to alignment around 100 sequences of SARS-CoV-2, and I think maybe you know about specific program for this work?

Well I found BasebyBase, this software is executed by Java and they described is specefic for virus genome.

Do you know about BasebyBase?

Thanks!

Sorry Joel Torres Villena , I haven't done any viral sequencing so I'm unfamiliar!

Thanks for your answer. I solved that and realize the mapping with Bowtie. I have an other question. Is possible calculated the binding energy between miRNA and genome reference? If it's possible, which software I can use?

I saw MiRTarget, but I don't know how to use.