alignment of many sequences

Question

[222aksg]

Has anone ever tried to align many sequences per say 300 sequences all together ?

[Devon Ryan]

Are you asking about "multiple sequence alignment" or something else?

[kloetzl]

The number of sequences is only one dimension. What about their length? Do you want to align whole genomes or single genes?

[Neilfws]

They sure have - but what types of sequences did you mean?

[cyril-cros]

Short answer, yes, using clustalOmega and around one thousand 10000pb closely related DNA sequences. The thing is, using lots of very long sequences means that visualizing your alignment with a tool like Seaview/Jalview is awkward.

What type of sequences are they (dna/protein, same species/gene family or not), do they differ a lot, and what do you want to achieve with them (build an HMM, do phylogenetics..)?

Answer 1

[Tanvir Ahamed]

You can use MAFFT

[Suzanne]

Have you tried Jalview? It is a free open source software from University of Dundee that is easy to launch. There is a suite of YouTube videos to help you to use it, they can be viewed from the web site http://www.jalview.org/training/Training-Videos.

Answer 2

[Suzanne]

Jalview is a free protein and nucleic acid sequence alignment visualisation software that can align hundreds of sequences. I suggest you check out the YouTube Jalview On-Line training videos at https://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfw. The program can be launch from http://www.jalview.org/.

[Michael]

Hi Suzanne, please don't post multiple identical or near identically worded answers to multiple questions. I take it that you are from the same institute or part of the development team, but still.