Introduction

KaKs_Calculator is a program that calculates nonsynonymous (Ka) and synonymous (Ks) substitution rates through model selection and model averaging. In addition, several currently acknowledged methods for estimating Ka and Ks are also incorporated into it.

The KaKs_Calculator package, including source codes, compiled executables and documentation, is freely available for academic use only at here.

Installation

For high efficiency and compatibility with more platforms, the kernel codes of KaKs_Calculator are written in standard C++. For Windows version we use Visual C++ 6.0 for GUI (Graphics User Interface). And for MAC version we use Objective C for GUI.

Linux/Unix

KaKs_Calculator has been tested on AIX, IRIX and Solaris.

MAC

KaKs_Calculator has been tested on MAC OS X version 10.6.6.

Methods for Calculating Ka and Ks

Calculating Ka and Ks normally involves three steps. Let us assume that the number of lengths between two DNA sequences compared is n and the number of substitutions between them is m. To calculate Ka and Ks, we need to count the numbers of synonymous (S) and nonsynonymous (N) sites (S + N = n) and the numbers of synonymous (Sd) and nonsynonymous (Nd) substitutions (Sd + Nd = m). Then it is after correcting multiple substitutions that (Nd/N) and (Sd/S) could represent Ka and Ks, respectively, since the observed number of substitutions underestimates the real number of substitutions as sequences diverge over time. Therefore, we can conclude from mentioned above that these methods normally involve three steps to estimate Ka and Ks: counting S and N, counting Sd and Nd, and correction for multiple substitutions.

Methods for calculating Ka and Ks adopt different substitution models with subtle yet significant differences. They can be classified as approximate methods and maximum-likelihood methods. Different from approximate methods, maximum-likelihood methods adopt the probability theory to finish all three steps mentioned above in one go.

Approximate Methods

There are several approximate methods incorporated into KaKs_Calculator, and we list their abbreviations in the program and their corresponding reference(s) as follows.

Maximum-Likelihood Methods

The method of GY takes account of sequence evolutionary features, such as transition/transversion rate ratio and nucleotide frequencies (reflected in the HKY Model) and incorporates these features into a codon-based model. We extend this method to a set of candidate models in a maximum likelihood framework and use the AICc for model selection and model averaging.

Model Substitution Rates Nucleotide Frequency
JC
F81
rTC=rAG=rTA=rCG=rTG=rCA Equal
Unequal
K2P
HKY
rTC=rAG ≠ rTA=rCG=rTG=rCA Equal
Unequal
TrNEF
TrN
rTC ≠ rAG ≠ rTA=rCG=rTG=rCA Equal
Unequal
K3P
K3PUF
rTC=rAG ≠ rTA=rCG ≠ rTG=rCA Equal
Unequal
TIMEF
TIM
rTC ≠ rAG ≠ rTA=rCG ≠ rTG=rCA Equal
Unequal
TVMEF
TVM
rTC=rAG ≠ rTA ≠ rCG ≠ rTG ≠ rCA Equal
Unequal
SYM
GTR
rTC≠rAG≠rTA≠rCG≠rTG≠rCA Equal
Unequal

rij: substitution rate between i and j, where i ≠ j and i, j∈{A, C, G, T}

Format of Sequence

KaKs_Calculator accepts quasi-AXT sequence format as follows. Before calculation, gaps and stop codons between compared sequences will be removed. You can also see “example.axt” in the folder of “KaKs_CalculatorXXX/examples/”.

For example:

NP_000026
ATGCTCCTGTG-CCACTGGCC
ATCCCC-TGCGCTCACTGGAC
NP_000053
ACAGaTtCTACCc-GCCcACTA--GgtGtt
---ggTTCTCCtACCcA-G-CACTACTggg

Each pair of sequences in an AXT file contains three lines: one sequence name line and two sequence lines. Any pairwise sequence is separated from one another by one blank line.

Parameters setting

Linux/Unix

KaKs_Calculator are more suitable for a large number of dataset to calculate Ka and Ks. It reads a pair of sequences and computes corresponding estimates one by one, so that it requires memory proportional to the maximum length among pairwise sequences. In addition, KaKs_Calculator allows user to choose more than one method to calculate Ka and Ks at one running time. The following is the parameters’ setting in Linux version.

For example

Windows

The Windows version provides users with a friendly interface to select input sequences’ file, genetic code and method(s) for estimating Ka and Ks. During calculating you can minimize the application window and send it to tray. After finishing calculation, KaKs_Calculator allows users to export results to file or clipboard at will.

Output Format

KaKs_Calculator provides comprehensive information estimated from compared sequences, including numbers of synonymous and nonsynonymous sites, numbers of synonymous and nonsynonymous substitutions, GC contents, maximum-likelihood score, and AICC, in addition to synonymous and nonsynonymous substitution rates and their ratio. Meanwhile, Fisher’s exact test for small sample is applied to justify the validity of Ka and Ks calculated by these methods.

Acknowledgements

We thank Professor Wen-Hsiung Li for providing us with his computer program and Professor Ziheng Yang for his invaluable source codes in PAML. We are grateful to Heng Li for his advice and Yafeng Hu for his help in software designing. We also thank all anonymous users for reporting bugs and sending suggestions.

Reference

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