Questions pertaining to genome-wide association studies.

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What free software is the best for the alignment and phylogenetic tree construction from the two or more .fasta whole genome sequence files?

What free software is the best for the alignment and phylogenetic tree construction from two or more .fasta whole genome sequence files? I have tried to run alignment using CLC Genomics workbench ...
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Phenotype choice for one of a MZ twin pair in a genetic association study

I was having a discussion with a colleague and this question came up... It is commonplace in molecular genetics studies to only genotype one of a pair of monozygotic twins (and then implicitly impute ...