So I have 2000 sequences I am aligning to identify comonalities. Firstly I am using different MSA programs (clustalo, muscle and MAFFT) and then converting them to a hmmprofile so I can view using skylign (hmm logo program).
Currently each MSA program is providing drastically different results. The differences range from the number of bases they are using (all sequences are between 24 and 55 but when viewing it goes up to 150) to the differences in bases seen with clustalo stating there is a TA motif at the begining and muscle saying its a GT for example.
This is my first time using MSA and this has left me wondering what I have done wrong to get such drastically different results.
I am using the default settings on each program.
Any help / advice would be greatly appreciated.
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