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.
alignment of many sequences
2 answers
You can use MAFFT
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Tanvir Ahamed
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/.
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.
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Michael Dondrup
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Are you asking about "multiple sequence alignment" or something else?
The number of sequences is only one dimension. What about their length? Do you want to align whole genomes or single genes?
They sure have - but what types of sequences did you mean?
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..)?