Can any one help me finding best tool for Multiple sequence alignment for about 49 sequences.. I need to find out in what what percent they are homologous to each other? I am currently using CLC sequence viewr and mega 6. It helps in aligning sequences but doesnot tell about percentage.
You are using wrong tool for wrong purpose. Use pairwise alignment to get the percentage similarity on pairs.
You will not get percentage similarity for MSA with any tool.
Check this list of tools.
http://www.genomecompiler.com/5-essential-tools-in-your-sequence-alignment-software/
https://www.ebi.ac.uk/Tools/msa/clustalo/
I think ClustalOmega is best fit for you.
Abhijeet Singh Sir I have total 49 unknown sequences and I need to eliminate and choose the best one. for this I make groups of sequences belonging to similar category. Now my 1 groups contains 6 sequences belonging to different ketoacylcoA synthase enzymes ( kCS 6, 8, 9, 22 etc)..I need to to pick the best one among them and for that I need alignment/homology percentage.. Pairwise alignment done if you have two sequences . It would laborious if I do pairwise for all those sequences.. I hope now you will understand my query
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