kakusan: a computer program to automate the selection of a nucleotide substitution model and the configuration of a mixed model on multilocus data

Abstract

The application of different substitution models to each gene (a.k.a. mixed model) should be considered in model-based phylogenetic analysis of multigene sequences. However, a single molecular evolution model is still usually applied. There are no computer programs able to conduct model selection for multiple loci at the same time, though several recently developed types of software for phylogenetic inference can handle mixed model. Here, I have developed computer software named ' KAKUSAN ' that enables us to solve the above problems. Major running steps are briefly described, and an analysis of results with KAKUSAN is compared to that obtained with other program.

Cytogenetic and DNA barcoding reveals high divergence within the trahira, Hoplias malabaricus (Characiformes: Erythrinidae) from the lower Amazon River

“…Either complementary analysis was processed with MEGA v.5 and statistical support for the nodes was provided by a Bootstrap test with 1000 pseudoreplicates (Felsenstein, 1985). For the ML inference the best substitution model to explain the variation in the data was chosen by KAKUSAN v.4 (Tanabe, 2007), based on the Akaike Information Criteria (AIC).…”

Systematic relationships of Oriental tiny frogs of the family Microhylidae (Amphibia, Anura) as revealed by mtDNA genealogy

“…Transitions and transversions were equally weighted, and gaps were treated as missing data. ML analyses were performed by Treefinder version June 2007 (Jobb et al, 2004), with the general time-reversible (GTR) model of DNA evolution with a gamma shape parameter (G), identified as the best-fitting model under the Akaike information criterion implemented in Kakusan 3 (Tanabe, 2007). BI and Bayesian posterior probabilities (BPP) were estimated using MrBayes 3.0b4 (Huelsenbeck and Ronquist, 2001), under the GTR model with G and proportion of invariable sites (I), selected by MrModeltest2.2 (Nylander, 2004).…”

<i>Ulva partita</i> sp. nov., a Novel <i>Enteromorpha</i>-Like <i>Ulva</i> Species from Japanese Coastal Areas

“…Phylogenetic analyses were performed using the maximum likelihood (ML) method in TREEFINDER (Jobb et al 2004), and Bayesian inference (BI) was performed using MrBayes 3.1.2 (Ronquist and Huelsenbeck 2003). Model tests for each analysis were performed using KAKUSAN 4.0 (Tanabe 2007). The best-fit models of nrITS2 were HKY+G, and that of the first, second, and third codon of the rbcL gene were F81+G, JC69+G, and GTR+G based on Bayesian information criteria.…”