Progressive multiple sequence alignment ClustalW is a widely used heuristic method for computing multiple sequence alignment (MSA). It has three stages: distance matrix computation using pairwise alignment, guide tree reconstruction using neighbor-joining and progressive alignment. To accelerate computing for large data, the progressive MSA algorithm needs to be parallelized. This research aims to identify, decompose and implement the pairwise alignment and neighbor-joining in progressive MSA using message passing, shared memory and hybrid programming model in the computer cluster. The experimental results obtained shared memory programming model as the best scenario implementation with speed up up to 12 times.

ABSTRACT Center for Technology Service (Pusyantek) in Agency for The Assesment and Application of Technology (BPPT) has two kinds of employee, there are civil and non-civil servants. The civil servants already have the official website for attendance system, but the non-civil servants don’t have the official website. The presence process for employee has engaged by the fingerprint machine, but still need help from Microsoft Excel. Administrator creates a recapitulation constantly for a period. This process can cause an inacurate data, inefficient time management, and others. Employees also hard to check the presence’s datas and complete the absences. With such problems, administrator needs attendance system that can help administrator and non-civil servants. The system was built by incremental method because the client already know requirements that the system necessary. Incremental method consist of five steps, those are communication, planning, modelling, construction, and deployment. System building involved two users, admin and employee. The system building engage by two iteration, which is first increment with 22 functions and second increment with 28 functions. System building successfully implemented attendance data management feature, attendance feature, filling permit’s data feature, and filling leave’s data feature.   ABSTRAK Badan Pengkajian dan Penerapan Teknologi (BPPT) khususnya di Pusat Pelayanan Teknologi (Pusyantek) memiliki tenaga kerja yang terdiri atas pegawai PNS dan non-PNS. Pegawai PNS sudah memiliki web resmi untuk sistem kehadiran, namun pegawai non-PNS belum memiliki. Proses kehadiran sudah dilakukan dengan mesin fingerprint, namun pengolahannya masih dilakukan secara manual menggunakan bantuan aplikasi Microsoft Excel. Pengolah melakukan pengolahan untuk menghasilkan rekap secara berkala per periodenya. Hal tersebut bisa menyebabkan data yang tidak akurat, pemanfaatan waktu yang tidak efisien, dan lain-lain. Pegawai pun sulit untuk melihat data kehadiran dan melengkapi data ketidakhadiran. Dengan adanya permasalahan tersebut, pengolah mengharapkan adanya sistem kehadiran berbasis web yang memudahkan pengolah dan pegawai non-PNS Pusyantek. Sistem dibuat dengan menerapkan alur kerja yang terstruktur dari metode pengembangan incremental. Metode tersebut digunakan karena klien sudah mengetahui kebutuhan apa saja yang diperlukan. Metode incremental terdiri atas lima tahapan, yaitu komunikasi, perencanaan, pemodelan, pembuatan, serta penyebaran dan umpan balik. Pembuatan sistem melibatkan dua user, yaitu admin dan pegawai. Pembuatan sistem menghasilkan dua kali iterasi yaitu increment pertama dengan 22 fungsi dan increment kedua dengan 28 fungsi. Pembuatan sistem berhasil mengimplementasikan fitur pengelolaan data kehadiran, fitur kehadiran, fitur kelengkapan data pengajuan izin, dan fitur kelengkapan data pengajuan cuti.