KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies

Abstract

We present an integrated stand-alone software package named KaKs_Calculator 2.0 as an updated version. It incorporates 17 methods for the calculation of nonsynonymous and synonymous substitution rates; among them, we added our modified versions of several widely used methods as the gamma series including γ-NG, γ-LWL, γ-MLWL, γ-LPB, γ-MLPB, γ-YN and γ-MYN, which have been demonstrated to perform better under certain conditions than their original forms and are not implemented in the previous version. The package is readily used for the identification of positively selected sites based on a sliding window across the sequences of interests in 5’ to 3’ direction of protein-coding sequences, and have improved the overall performance on sequence analysis for evolution studies. A toolbox, including C++ and Java source code and executable files on both Windows and Linux platforms together with a user instruction, is downloadable from the website for academic purpose at https://sourceforge.net/projects/kakscalculator2/.

The SI Strain of Measles Virus Derived from a Patient with Subacute Sclerosing Panencephalitis Possesses Typical Genome Alterations and Unique Amino Acid Changes That Modulate Receptor Specificity and Reduce Membrane Fusion Activity

“…A phylogenic tree constructed using SI, IC-B, 9301B, WA.USA/17.98, and reference strains (66) was drawn using FigTree software. Ka/K s calculations were performed using KaKs Calculator version 2.0 software (64). Briefly, using the two nucleotide sequences of each protein-coding region, the nonsynonymous and synonymous substitution rates (Ka and K s , respectively) were calculated by counting the numbers of nonsynonymous and synonymous sites (NA and NS, respectively) and the numbers of nonsynonymous and synonymous substitutions (MA and MS, respectively).…”

Evolutionarily Conserved Alternative Splicing Across Monocots

“…Since these filtering processes resulted in , 100 SAST alignments associated with AltTE events, we focused only IntronR, ExonS, AltA, and AltD events for this analysis. Selection pressure on AS events at the amino acid level was measured by determining the Ka/Ks ratios using KaKs_Calculator2.0 through model averaging (Wang et al 2010), and functional constraints were measured with Ks value. To minimize errors introduced by alignments, or due to paralogs that may result when comparing loci across large phylogenetic distances, the Ka/Ks evaluation of conserved AS events was limited to those events originating within orthologous grass genome loci that also exhibit conserved synteny (defined above).…”

High quality reference genome of drumstick tree (Moringa oleifera Lam.), a potential perennial crop

“…To investigate which genes may be associated with certain traits that have made M. oleifera's successful, we conducted positive selection analysis. Blast and KaKs_Calculator [54] compared orthologs between M. oleifera and each one of Carica papaya, Vitis vinifera and Malus domstica, and respectively found 566, 399, 112 genes of M. oleifera with Ka/Ks ratio>1 (significance, P<0.05; see Table S11, Table S12, Table S13). We further found four genes that overlap among the three gene sets (Figure 2).…”