Konstruksi Dan Perbandingan Pohon Filogenetik Isolat SARS-CoV-2 Menggunakan Metode Maximum Parsimony Dan Maximum Likelihood

Putri, Anisa Ardiani (2026) Konstruksi Dan Perbandingan Pohon Filogenetik Isolat SARS-CoV-2 Menggunakan Metode Maximum Parsimony Dan Maximum Likelihood. Other thesis, Institut Teknologi Sepuluh Nopember.

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Abstract

Pandemi COVID-19 yang disebabkan oleh Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) mendorong perlunya analisis filogenetik untuk memahami hubungan kekerabatan dan pola evolusi virus. Penelitian ini bertujuan mengonstruksi serta membandingkan pohon filogenetik SARS-CoV-2 menggunakan metode Maximum Parsimony (MP) dan Maximum Likelihood (ML). Dataset yang digunakan terdiri atas 990 isolat sekuens genom lengkap SARS-CoV-2 yang mewakili 26 klasifikasi varian World Health Organization (WHO) dan delapan clade utama GISAID (G, GH, GR, GRA, GRY, GK, GV, dan O ) dari tujuh wilayah geografis dunia. Selain itu, digunakan pula 9 sekuens outgroup dari coronavirus terkait yang diperoleh dari basis data NCBI. MSA dilakukan menggunakan MAFFT dan menghasilkan alignment sepanjang 43.212 bp dengan 16.539 situs parsimoni-informatif (38,27%). Konstruksi pohon MP menggunakan algoritma Parsimony Ratchet, sedangkan pohon ML dibangun berdasarkan model substitusi nukleotida terbaik yang dipilih melalui Akaike Information Criterion (AIC). Hasil seleksi menunjukkan bahwa General Time Reversible (GTR) merupakan model terbaik dengan nilai AIC 634.183,49. Pohon MP menghasilkan Tree Length minimum sebesar 57.842 langkah, sedangkan pohon ML menghasilkan nilai log-likelihood sebesar −315.087,744. Validasi topologi dilakukan menggunakan bootstrap 1.000 replikasi secara identik pada kedua metode. Hasil analisis menunjukkan bahwa kedua metode menghasilkan pengelompokan utama yang konsisten dengan klasifikasi varian WHO maupun clade GISAID, dengan dominasi isolat pada clade GRA yang mencerminkan penyebaran luas varian Omicron. Namun, terdapat perbedaan topologi yang cukup besar antara kedua pohon, ditunjukkan oleh nilai Robinson–Foulds Distance sebesar 1.488. Selain itu, metode ML menghasilkan dukungan bootstrap yang lebih tinggi dibandingkan metode MP. Dengan demikian, metode ML dinilai lebih unggul dalam merepresentasikan proses evolusi SARS-CoV-2 karena mampu mengakomodasi model substitusi nukleotida yang lebih realistis dan memberikan dukungan statistik yang lebih kuat.
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The COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has driven the need for phylogenetic analysis to understand the evolutionary relationships and patterns of the virus. This study aims to construct and compare SARS-CoV-2 phylogenetic trees using Maximum Parsimony (MP) and Maximum Likelihood (ML) methods. The dataset used consists of 990 whole-genome sequence isolates of SARS-CoV-2 representing 26 World Health Organization (WHO) variant classifications and eight major GISAID clades (G, GH, GR, GRA, GRY, GK, GV, and O) from seven geographical regions worldwide. In addition, 9 outgroups sequences of related coronaviruses obtained from the NCBI database were also used. Multiple Sequence Alignment (MSA) was performed using MAFFT, resulting in an alignment length of 43,212 bp with 16,539 parsimony-informative sites (38.27%). The MP tree construction utilized the Parsimony Ratchet algorithm, while the ML tree was built based on the best nucleotide substitution model selected through the Akaike Information Criterion (AIC). The selection results indicated that the General Time Reversible (GTR) was the best model with an AIC value of 634,183.49. The MP tree produced a minimum Tree Length of 57,842 steps, whereas the ML tree generated a log-likelihood value of −315,087.744. Topological validation was performed using 1,000 bootstrap replications identically applied to both methods. The results showed that both methods successfully grouped the sequences according to GISAID clades. Most isolates belonged to the GRA clade, reflecting the widespread transmission of the Omicron variant. Despite this similarity, the two trees had notable structural differences, with a Robinson–Foulds distance of 1,488. Since the ML method provided higher bootstrap support and uses a more realistic nucleotide substitution model, it is better suited for representing the evolutionary history of SARS-CoV-2.

Item Type:	Thesis (Other)
Uncontrolled Keywords:	Pohon Filogenetik, Maximum Likelihood, Maximum Parsimony, Model Substitusi Nukleotida, SARS-CoV-2, Multiple Sequence Alignment, Phylogenetics Tree, Maximum Parsimony, Maximum Likelihood,Nucleotide Substitution Model
Subjects:	Q Science > QA Mathematics Q Science > QA Mathematics > QA274.2 Stochastic analysis Q Science > QA Mathematics > QA274.7 Markov processes--Mathematical models. Q Science > QH Biology > QH426 Genetics Q Science > QR Microbiology Q Science > QR Microbiology > QR355 Virology
Divisions:	Faculty of Science and Data Analytics (SCIENTICS) > Statistics > 49201-(S1) Undergraduate Thesis
Depositing User:	Anisa Ardiani Putri
Date Deposited:	31 Jul 2026 06:28
Last Modified:	31 Jul 2026 06:28
URI:	http://repository.its.ac.id/id/eprint/140814

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