If your nucleotides are codons then the best choice is PRANK, then MAFFT with high accuracy settings. Other aligners will perform worse. See for example Fletcher & Yang Mol biol Evol 2010 for a benchmark.

If they are not codons, I would align it with t-coffee, MUSCLE and MAFFT and would retain the consensus before going through manual curation.

clustal w alignment at EBI but that take of may not be more than 200 sequence.

What about BWA?

I think clustal W (ebi.ac.uk) is the easiest one for you. you can show the sequence in colours as well.

Try bioedit or mega 5.

If it is available you can also try Megaling (lasergene) or CLC workbench or Bionumerics.

Mega 4, mega 5. At ebi-clustalw2, muscle, t-coffee.

ClustalW or SeaView....

clustalW or mafft or t-coffee or muscle

You ma also want to check out FSA http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000392

Thank you everyone ,, but most of the above mentioned tools are restricted to 100 to 200 sequences

i m having 500 sequences :(

@brandon - Fsa takes only 100 sequences.

hope Bionumeric can do it,, stil i havent try it.

I do not know for sure if FSA will work well with 500 sequences, however the text on the page was "Be aware that the webserver may reject alignment jobs which contain many (> 100) sequences due to computational limitations. If you wish to align many sequences, then please download and install FSA in order to run the alignment on your personal computer", which makes me think the 100 sequence limit this was specific to their public web server.

If you don't have luck elsewhere, maybe you can try installing it on your own system.

My recommendation is 'JalView'.

If your nucleotides are codons then the best choice is PRANK, then MAFFT with high accuracy settings. Other aligners will perform worse. See for example Fletcher & Yang Mol biol Evol 2010 for a benchmark.

If they are not codons, I would align it with t-coffee, MUSCLE and MAFFT and would retain the consensus before going through manual curation.

I forgot: DO NOT USE clustal it is completely outdated and outperformered by the more recent aligners.

You can also use Praline sequence alignment tool.

(http://www.ibi.vu.nl/programs/pralinewww/)

I usually use cluatalw program with command line options on Linux. If you're planning to align many sequences, Linux system is much fater and stable than Windows system.

Here is a link to a set of sequence alignment programs.

http://tcoffee.crg.cat.

you can use Clustalx, Bioedit and the jalview for this. I has did that in a archive with more than 100 sequences and he did the alignment

MUSCLE or TCOFFE are the better tool to perform MSA

I would suggest you to opt for MAFFT or Seaview.

Clustalx... http://www.clustal.org/

State of the art seems to be this one by the Söding group @ LMU Munich:

"HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment"

Michael Remmert, Andreas Biegert, Andreas Hauser & Johannes Söding

(quote) "Compared to the sequence-search tool PSI-BLAST, HHblits is faster owing to its discretized-profile prefilter, has 50–100% higher sensitivity and generates more accurate alignments."

http://toolkit.genzentrum.lmu.de/hhblits/

Bioedit, clustalx, mega, meme

Thank you Everyone , ..for valulable Suggestions .

The best option (the usual we use in metagenomics) is MAFFT.

Clustalw2,muscle

if its a protein u can try Phyre 2 server. it will also produce tentative 3d strusture for ur protein. the dataset is set to global be default. U can also use MEGA which includes Muscle for allignment. exports in multiple formats and supports protein and dna sequences both

Clc genomics workbench are useful for msa

http://www.ebi.ac.uk/Tools/msa/ go to this link depend upon ur choice of interest...

a lot of tools are available for MSA....best is the clustal w,clustal x and t-coffee alignments.....and for the viewing of tree ,u can you treeview or pylip.

You have a free platform of tools called Ugene with a lot of options. Very user friendly.

CLUSTAL is a general purpose global multiple alignment program for DNA or proteins. It produces biologically meaningful multiple alignment of divergent sequences

It calculates the best match from the selected sequences and aligns them so that the identities, similarities and differences can be seen. Evolutionary relationships can be seen via viewing cladograms or phylograms

CLUSTAL was developed by Thompson et al (1994). Clustal W is the latest version of Clustal W stands for weighing – ability of the program to provide weights to sequence and program parameters. Clustal X provides graphical interpretation also.

Clustal W is a general purpose multiple sequence alignment program for DNA or proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. Evolutionary relationships can be seen via viewing Cladograms or Phylograms.(online T00l)

ClustalX is a new windows interface for multiple sequence alignment programs. Clustal uses a method called pairwise progressive sequence alignment. This heuristic method first does pairwise sequences alignment for all the sequence pairs that can be constructed from the sequence set. A dendrogram (guide tree) of the sequences is then done according to the pairwise similarity of the sequences. Finally a multiple sequence alignment is constructed by aligning sequences in the order, defined by the guide tree.(offline Tool)

MEGA is an integrated tool for automatic and manual sequence alignment,

inferring phylogenetic trees, mining web-based databases, estimating rates

of molecular evolution, testing evolutionary hypotheses, Estimating Evolutionary Distances and Marking Genes/Domains. For MEGA, all input data files are basic ASCII-text files, which may contain DNA sequence, protein sequence, evolutionary distance, or phylogenetic tree data. After creating the file, you should change this extension to .MEG, so that you can distinguish between your data files and the other text files.

You can use ClustalW

Clustal (http://www.clustal.org/) is the most balanced (speed / quality). t-coffee (http://www.tcoffee.org) is good too but not so easy to use. For other manipulations MEGA (www.megasoftware.net/) is the best. Everything is free ...

On nucleotides, all these software are equally limited. I would recommend using the M-Coffee mode of T-Coffee that makes it possible to combine the output of several aligners. In theory, the resulting alignments should be a bit more accurate, but the real point is that this approach will show you where the aligners agree on the final MSA, thus making it possible to cut out columns.

On the command line, use: t_coffee -seq -method clustalw_msa mafft_msa muscle_msa -output aln,score_html, score_ascii

The score_ascii output can the be used to programmatically extract the columns having the highest level of agreement among the methods (see documentation).

Overall, in terms of accuracy, mafft, probcons, and T-Coffee are among the most accurate. ClustalW has been shown to have a lower accuracy. It is still disputed wether prank or Sate and other so-called 'phylogenetic aligners' produce improved sequence alignments. On protein sequences they do not, as judged from structure based references.