Hi Rhiannon.

Against many of the comments above, first I have to ask about what you really need to do and how many sequences do you have.

First of all, what do you mean with clean sequences?

If you have to search for ambiguous bases you'd probably prefer to see chromatograms beneath your sequences, so you can see which one have the best signal and, just in case, correct them. For this purpose I think the best one is Chromas. Other one you can correct your sequences with (quite easy) before you do your alignments is SeqMan.

To achieve a good alignment I use MUSCLE. As far as I have tried many aligners, I think is the best, the fastest and (probably) the one with the more efficient algorithm. I also work with MAC and you can download a 'Terminal-using' version very easy to use. It will also work with big datasets as the ones from next-gen sequencing.

And if you want to correct your sequences after having them aligned I will recommend BioEdit as well as some of our colleagues. It is easy and very visual, but, if I am not wrong, I think it only work in Windows. Maybe you will have to think on installing a Virtual Machine with Windows on your MAC. Sometimes it is very useful.

If you need to clean sequences not individually, but from a large dataset, and the cleaning means to delete short ones, the ones with homopolymers or the ones with numerous 'Ns' I would recommend to use MOTHUR. Maybe you will have to train yourself a little bit before its use, but after a couple of hours you will see that it is very intuitive and very useful for many things.

Thanks for reading and good luck!

What do you mean by "aligning"? Do you want to create an assembly against a reference genome or do you want to create a (multiple) sequence alignment?

Geneious is nice if you are a user who wants an out of the box tool and can afford it.

Just google "Phylogeny programs" and the first reference will give you a large collections of programs. You will find in categories what you need. Jalview is not bad to my mind but there are many others...

ClustalW is another good option http://www.ebi.ac.uk/Tools/msa/clustalw2/

it's a web-based open source, you just need to insert your sequences in FASTA format.

You may to use different sofware depend what datasets you want to analyse. For aligning and redaction of your sequences you may to use some of them: ClustalW, BioEdit, Paup, Staden, Genedoc etc. Some of them are free. You also can to use online services for this procedure i.e. MUSCLE or something else.

I like the CLC Genomics Workbench, from CLC Bio. It has a very friendly interface and is available for Mac! ;)

I work on Linux OpenSUSE 12.1. For me, best alignment tool is standalone ClustalW2, while for cleaning up, standalone CD-HIT is best suited to me.

You can make a multiple sequence alignment (MSA)with ClustalW (because everybody uses it) and/or MUSCLE (because it is very. You can also Creat and comparing multiple sequence alignments with Tcoffee (because it is very accurate and combine sequences and structures).

Take a look at the attached paper for more information about MSA programs

Article Assessment of molecular (dis)similarity: The role of multipl...

Hi

I personally agree with many of the proposals: MUSCLE, CLUSTALW2, etc are great softwares. But because I am getting old, I love this very classic software called Multalin. You have a server and it is quite powerful in the results. Give a try at :

http://multalin.toulouse.inra.fr/multalin/

It has several utilities and links to other softwares.

Good luck. Best. Paco

Dear Morris

For aligning your sequences you may use any one of the programs mentioned below

ABA, ALE, AMAP, Anon., BAli-Phy, CHAOS/DIALIGN, ClustalW, CodonCode Aligner, Compass, DIALIGN-TX and DIALIGN-T

DNA Alignment, DNA Baser Sequence Assembler, EDNA, FSA, Geneious, Kalign, MAFFT, MARNA, MAVID, MSA, MSAProbs

MULTALIN, Multi-LAGAN, MUSCLE, Opal, Pecan, Phylo

Best Regards

Jalview ,ClustalW, biological workbench

I always liked the ClustalW program

I may try out clustalW. Seems to be a popular one. Thank you for all the suggestions and help.

CLC workbench clean up is a bit tricky, I know it has good graphics but not very good with fast clean up.

Have you tried Lasergene? Megalign woks well.

ClustalW ans ClustalX (downlable on the PC) are useful but do not forget to adjust eventually some parameters. It depends on the closeness of sequences you have to be aligned. Using defaults parameters, bad scores are assigned to the gaps or insertions, because these programs make a global alignment. If the sequences are distantly related, prefer local alignment programs, as DIALIGN. If the conserved parts of the sequences are embedded with highly divergent parts, DIALIGN will manage the situation.

Geneious for sure! Clustal is included in it!

Hi, If you need to read your sequence and align with a ref seq, very easy tool, also for mac, Chromas Pro, available free for 30 days is a good tool

You try MATLAB Bioinformatics tool box. It is very good but need some training

Article A Comprehensive Study by Using Different Alignment Algorithm...

For larger datasets I usually use MUSCLE option in MEGA software, it is very fast. For smaller datasets, GenDoc is more user-friendly. Both software are free. For cleaning up sequence files, trimming and assembling multiple segments of a sequence , I think DNA Star Lasergene (SeqMan) is the best.

I prefer MEGA 6

CLC Main Workbench 6 and MEGA6 are useful tools to align and clean up sequences

Hi Rhiannon.

Against many of the comments above, first I have to ask about what you really need to do and how many sequences do you have.

First of all, what do you mean with clean sequences?

If you have to search for ambiguous bases you'd probably prefer to see chromatograms beneath your sequences, so you can see which one have the best signal and, just in case, correct them. For this purpose I think the best one is Chromas. Other one you can correct your sequences with (quite easy) before you do your alignments is SeqMan.

To achieve a good alignment I use MUSCLE. As far as I have tried many aligners, I think is the best, the fastest and (probably) the one with the more efficient algorithm. I also work with MAC and you can download a 'Terminal-using' version very easy to use. It will also work with big datasets as the ones from next-gen sequencing.

And if you want to correct your sequences after having them aligned I will recommend BioEdit as well as some of our colleagues. It is easy and very visual, but, if I am not wrong, I think it only work in Windows. Maybe you will have to think on installing a Virtual Machine with Windows on your MAC. Sometimes it is very useful.

If you need to clean sequences not individually, but from a large dataset, and the cleaning means to delete short ones, the ones with homopolymers or the ones with numerous 'Ns' I would recommend to use MOTHUR. Maybe you will have to train yourself a little bit before its use, but after a couple of hours you will see that it is very intuitive and very useful for many things.

Thanks for reading and good luck!

ClustalW is not longer being mantained and updated by EMBL. Is much better to try the new version called clustal omega for align sequences. (DNA, RNA and proteins)

Hi Rhiannon- I don't know how many sequences you're dealing with, but if it's a relatively small number that you're dealing with manually, then you can download (for free) the "CLC Sequence Viewer" software from CLC Bio (www.clcbio.com). It's quite easy to use and includes a very robust sequence alignment algorithm, plus the option to download additional alignment programs (also for free). It will import sequences of a variety of formats. If you're having to deal with large numbers of sequences then you'll probably need to go with a commercial product and pay the price. Hope that helps.