Judul: Performance Comparison Between Kimura 2-Parameters and Jukes-Cantor Model in Constructing Phylogenetic Tree of Neighbour Joining (NJ)
Abstrak: Bioinformatics as a recent improvement of knowledge has made an interest for scientist to collect and analyze data to provide the best estimate of the true phylogeny. The objective of this research is to construct and compare the phylogenetic tree of Neighbour Joining (NJ) based on different models (Kimura 2-Parameters and Jukes-Cantor) and to find out which model is more reliable on constructing NJ’s tree. In order to build the tree, reliable set of data is conducted from D-loop mtDNA sequences that is available in Gen Bank. The nucleotide sequences come from Bison bison (American bison), Bos taurus (European cow such as Shorthorn), Bos indicus (zebu breeds), Bos grunniens mutus (one of subspecies of cow), and Capra hircus (species of goat). The reliability of each models was measured using the Felsentein’s bootstrap method. The whole bootstrap process for each models was repeated 1.000, 5.000, and 10.000 times to detect its reliability. The performance was measured on the basis of the consistency of the topology relationship, the stability of nodes, the consistency of bootstrap confidence level (PB), standard error of distance, change of PB from (1.000-5.000) to (5.000-1.000), computational time, and BIC score. NJ’s phylogenetic tree with kimura 2-parameters and jukes cantor model have a good node stability and is also generally successful in representing topological relationships between taxa. The increasing of bootstrap replication number in common will increase the consistency of bootstrap confidence value ( . It means both models have a good reliability. But, when the number of sequences is large and the extent of sequence divergence is low, it is generally difficult to construct the tree by any models. In conclusion, Kimura 2-Parameters has a better performance than Jukes-Cantor.
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Judul: Analysis of Long-Read Sequences DNA on Merbau (Intsia bijuga), Sandalwood (Santalum album), and Moringa (Moringa oleifera)
Abstrak: Informasi genetik dapat digunakan dalam upaya konservasi dengan menduga keragaman genetik melalui penggunaan marka genetik. Sekuens DNA dapat diperoleh melalui tahap ekstraksi, isolasi, dan sekuensing. Sekuensing dapat dilakukan menggunakan mesin dengan teknologi terbaru seperti teknologi ONT, namun jarang sekali diaplikasikan pada pohon hutan. Penelitian ini bertujuan untuk mendapatkan sekuens DNA dan melakukan analisis filogenetik beberapa jenis pohon hutan, yaitu merbau (Intsia bijuga), cendana (Santalum album), dan kelor (Moringa oleifera). Tahapan penelitian mencakup perolehan data hasil sekuensing dan basecalling, quality check, assembly, polishing, anotasi, analisis kekerabatan, serta konstruksi pohon filogenetik. Analisis kekerabatan dilakukan menggunakan DNA sekuens berupa intergenic spacer trnH-psbA, accD, dan matK. Hasil analisis kekerabatan menunjukkan bahwa pohon filogenetik jenis merbau, cendana, dan kelor memiliki nilai bootstrap yang bervariasi yaitu masing-masing sebesar 0,965 (96,5%), 0,509 (50,9%), dan 0,798 (79,8%).
Keyword: accD, analisis filogenetik, long-read sequence, matK, trnH-psbA

Judul: Pengeringan Lada Putih (Piper nigrum Linn.) Menggunakan Oven Gelombang Mikro (Microwave Oven)
Abstrak: Peranan lada dalarn perekonomian Indonesia terbilang penting, yaitu sebagai komoditas ekspor non migas penghasil devisa. BPEN (2001) mencatat pada tahun 2000 porsi Indonesia dalarn nitai ekspor lada dunia sebesar 32.21 %. Masalah yang dihadapi oleh negara-negara pengekspor lada adalah pencemaran mikroba serta menurunnya minyak atsiri akibat pengolahan. Pengeringan merupakan metode yang efektif untuk pengolahan produk pertanian. Peranan pengeringan dielektrik, dengan menggunakan gelombang elektromagnetik langsung ke posisi molekul air dapat mengurangi kerusakan produk.
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