Use of amino-acid sequences versus use of nucleotide sequences in phylogenetic analysis
In general, many sequence alignment programs can use multiple substitution models, distinguishing between nucleotides, amino acids, and codons. A protein sequence has functional information that is not directly visible in the nucleotide sequence. 

The papers you link deal with horizontal gene transfer, where a gene is passed to more distant  organism. Different species have different codon usage biases, i.e. the translation efficiency is different for different codons. On one hand, this means that HGT is more likely to occur between species of similar codon usage. On the other hand, "codon usage of horizontally transferred genes approaches the host usage over time." Thus, on the nucleotide level, the phylogenetic signal will get lost due to the evolutionary pressure on translation efficiency, while on the protein level, there will be more conservation.