A phylogenetic tree may be built using morphological (body shape), biochemical, behavioral, or molecular features of species or other groups. In building a tree, we organize species into nested groups based on shared derived traits (traits different from those of the group's ancestor).
No it does not effect the temperature of boiling point
In nature there are many more variations amino acids than the simple 20 found in humans. However, when analyzing the human genome sequence, there is a code for all 64 permutations (4^3), only some of them share amino acids. This is a safe-guard against mutations of one or two nucleotides. For example, the amino acid Alanine is coded with four different nucleotide sequences: GCA, GCC, GCG, GCU. Also some amino acids code the same like UUU &UUC