Hi all apart from clustal omega what other tool can i use for aligning more than 4000 sequences?

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Muhammad Umar Zafar Khan

you can use Dendroscope software its specially designed for big data.

Victoria Pam

Thank you. i will use this later. any suggestions for one for multiple alignment

MAFFT is excellent for this task.

Kieran Boyce

Mafft is a good alternative, as is Muscle. It might be also worth looking at Kalign.

The Consistency alignment programs - TCoffee, MSAProbs, Mafft in G-INS-i mode, etc - are probably too slow for 4000 seqs, although they do give good results.

If the purpose of the alignment is phylogeny tree construction, then it might be worth looking at PRANK and PAGAN.

If you need to increase the number of seqs to many tens of thousands and speed is an issue, then the PartTree option in Mafft could be a good option, as well as FAMSA and UPP.

Overall, for this number of seqs I'd recommend Clustal Omega, Mafft or Muscle (Disclosure: I did my PhD in the lab that created Clustal Omega). The three programs are relatively easy to install, or you can do the alignments on the EMBL EBI servers.

Please feel free to contact me directly for any more details

Thank you both for your kind reply. i was trying to run away from learning new things but i can see i must. clustal 0 and Maft and Famsa are my options considering the number of sequences i have. Kieran i may need to contact u thank you. installing clustal omaga on my system is proving to be quite complex.

Hi Victoria

You need to install argtable2 before you install Clustal Omega. Please feel free to contact me directly with any installation problems you find.

You can also upload your sequences to the EMBL EBI servers and use their version of Clustal Omega https://www.ebi.ac.uk/Tools/msa/clustalo/. This might be an easier solution if you don't have many alignments to generate.

kieran

Hi Kieran , i have tried the version of Clustal Omega https://www.ebi.ac.uk/Tools/msa/clustalo/. how ever it can only do 4Mb and my file is larger than that. i will install the one that can handle more. thank you