I would like to calculate the differences between sequences and genetic distances and dissimilarity/similarity scores. Geneious was handy enough but it expired. Bioedit is anything else but user friendly. Also tried UGENE and MEGA. Anything else?
I like clustalw and clustalw-mpi (both free). The latter can align thousands of sequences on a multicore system if that is the sort of thing you're after. I have a perl script that calculates a matrix of % identities from an aligned fasta. You can message me if you would like to have the script.
PhyDE (http://www.phyde.de/) is a great alignment editor. It has superior functions fpr manual alignment (like drag-and-drop of blocks etc.). It uses MUSCLE (http://www.drive5.com/muscle/) as an add-in for initial automatic alignment.
Hi Georgolopoulos,
The alignment algorithm in T-Coffee and MUSCLE would be great for most of the sequence sets. You can easily get your sequence divergence by using the analysis tool in MEGA. Otherwise, you can get the genetic distance using distance analysis if you are familiar with the command in PAUP.
Cheers, HongChang
Hi, there are a lot of alignnent programs each with there own settings. Therefore it is important to realize this and compare different alignments. I myself have use clustalx or clustalw. Its easy to use through a server or download it as a stand alone. These two, and in particular clustalx are widely used. Furthermore, several phylogenetic software packages like mega have included it but also muscle. Good luck
I would recommend a very high speed alignment software called MAFFT, which you can find here (http://www.ebi.ac.uk/Tools/msa/mafft/). This performs well and you can tweak several parameters. I personally like to compare alignments from multiple runs in MAFFT. But it would be wise to compare MAFFT results with methods that accomplish a similar task using different approaches not based on fourier transform. Fortunately, the same website that hosts the online MAFFT interface linked to above--that of the European Bioinformatics Institute--also hosts a variety of other tools for multiple sequence alignment. Look for them by stepping to their alignment page, http://www.ebi.ac.uk/Tools/msa/. Just beware some software programs are not suitable for very large alignments. For quick sequence divergence calculations, I use MEGA5 or PAUP* like basically everyone else! Cheers.
Check Wikipedia's list (http://en.wikipedia.org/wiki/List_of_sequence_alignment_software). I like T-coffee, muscle and clustalw
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