This research aims to investigate visibility, Web Impact Factor (WIF), RWIF and the collaboration rate of the websites of the Iranian Universities dominated by the Ministry of Science, Research and Technology (MSRT), and Health and medical Education (MHRME), using an analysis of the various links among these websites and webometrics. From all 119 websites belonging to the Iranian Universities, due to some technical problems, only 111 ones were reviewed through Yahoo, in a period of one month (October 6 – November 5, 2008). These were decreased to 71 websites in analysing co-links and identifying hi-frequency websites. The data were collected in two phase: using Yahoo Directory, first all the investigated university websites were retrieved and stored on a PC. Second the websites' various links were extracted and analysed. The results indicated that among all universities, the website of Olume Behzisty University had the most and Medical Science of Qum, the least visibility (respectively with 6.44 and 0.08). The WIF of Medical Science of Shahrood Website was the most, and that of Medical Science of Rafsanjan website, the least one. In regard to RWIF, the website of Mohghegh Ardebili with 3.5 had the first, and those of three universities (Gilan, Medical Science of Shahid Beheshti, and Medical Science of Gilan) had the last rank. In-link analysis results showed that the investigated websites had collaborated in 9 clusters, and a multidimensional scale illustrated the collaboration of these websites in 9 clusters.
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