I am trying to make a phylogenetic tree using protein sequences. During the multiple alignment, for several pairs, pairwise distances could not be calculated, and therefore could not generate phylogenetic tree. When I remove these sequences from the alignments, now there are some other pairs for which sequence distances could not be calculated.
any suggestions?
Please try any other alignment tools used specifically for proteins.
To calculate pairwise distance you can use tools like MEGA5 or Phylip. You can feed the alignment file or the raw file to the program and get distance/tree for it.
Thanks Guys for your suggestions. well i tried earlier several program, all listed here with various combinations of scoring matrices and also played with the parameters but there were few problematic sequences. like in an alignment there are two sequences that were problematic and when you do alignment without these two sequences, using same parameters, now few other sequences were not aligned. anyway i played with several combinations and after removing 3 sequences, the alignment is good to make a phylogenetic tree. to have the correct answer, probably we need to look into how these scoring matrices work.
Dr. Sharma, I think you are right. Please select a appropriate alignment program and also not to go with default values of parameters.
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