## 5 Results and Evaluations
### Quality Assessment of the Alignment Results  
In this section, we compare the LF-EP FM aligner's performance with the original FM aligner and other state-of-the-art FM algorithms such as SOAP2, BOWTIE2, BWA, and GEM3. We use BALIBASE, OXBENCH, SABRE, and PREFAB benchmarks to evaluate alignment quality. These benchmarks are highly respected in sequence alignment because they effectively evaluate aligner performance with respect to different features of alignment accuracy. This aims to assess aligner effectiveness across multiple benchmarks under various scenarios and sequence attributes. The benchmarks have been converted to the universally accepted FASTA format (as short-read sequences), which facilitates the following analytical processes. In our evaluation, we use two accuracy metrics: Quality Score (QS) and Total Column Score (TCS). The QS measures the fraction of correct residue pairs aligned relative to the total number of residue pairs in the alignment. On the other hand, the TCS measures the correct alignment of columns relative to the total number of columns in the alignment. The TCS shows that the aligners are capable of reflecting the structural features of the sequences. The selection of the algorithms and the benchmarks is made in such a way that they represent a broad spectrum of methodologies for sequence alignment, allowing for the creation of a global assessment of the alignment performances of the aligners. The same FM-based algorithms are used in aligners tested in the benchmarks. Therefore, it might be expected that these various aligners would show slight differences in result quality. The absolute quantities QS and TCS are dimensionless; only their relative ratio is of interest. Table 4 illustrates the QS and TCS values computed for different benchmarks employed in the present study. Since the QS and TCS values are dataset-dependent, we assess their relative values to provide a comparative assessment of the effectiveness of different sequence aligners. From the analysis in Table 4, the proposed LF-EP-based FM aligner surpassed the rest, with the highest scores in both QS and TCS. Evaluation results reveal that the LF-EP-based FM aligner is among the most highly reliable and accurate FM aligners compared with previous aligners, thus signifying the ability to integrate the LF-EP algorithm into the framework of FM aligner. \begin{table}
\begin{tabular}{p{142.3 pt} p{142.3 pt}} \hline \hline
**Components** & **Details** \\ \hline Genome Reference & Human genome (id: HS37D5) from the international 1000 Genomes Project. Sizes are up to 3 GB. \\ \hline Short-Read Data & SRR766060 paired-end genome. Each segment is 8.7 GB in size. \\ \hline Benchmark Datasets & BALIBASE, OXBENCH, SABRE, and PREFAB. \\ \hline Sequence Simulation Tools & randDNA and wgsim. \\ \hline Alignment Algorithms & SOAP2, BOWTIE2, BWA, and GEM3. \\ \hline Experimental Setup & Two NUMA nodes: Intel Xeon and AMD Opteron. \\ \hline NUMA Node Specifications & Processors: 4 processors with 32 cores and 64 threads. \\  & Memory: 128 GB; NUMA Nodes: 4. \\ \hline Processor Details & AMD Opteron-6376: core network with full ties. \\  & Intel Xeon E5-4620: ring with circular connections. \\ \hline \hline \end{tabular}
\end{table} 
Table 3: Details of the configurations in the experiments. Furthermore, SOAP2 was observed to perform at almost the same level as the LF-EP FM aligner, albeit a little lower. It can be observed that QS and TCS scores of SOAP2 are the second highest across most benchmarks, indicating that this tool is quite promising and could improve its alignment performance with further development. Additionally, BOWTIE2 shows a small decrease in performance quality compared to SOAP2, suggesting it might be suboptimal for strict quality standards. BWA also shows a similar drop in performance to BOWTIE2 but maintains impressive QS and TCS scores consistently during the evaluations. This finding positions BWA as a practical choice based on particular task needs and circumstances.