以下のスクリプトは全て自由にお使いいただけますが，このスクリプトの解析結果については一切責任を負いません．もし何かバグやお気づきの点がありましたらmanozawa[at]tmu.ac.jpまでご連絡ください．
These scripts are freely available, but I do not take any responsibility of the results from these scripts. If you find any problems, please send an e-mail to manozawa[at]tmu.ac.jp. I really appreciate your feedback.
1. dS_dN. This file contains four perl scripts for conducting sliding window analysis for computing the rates of synonymous and nonsynonymous substitutions based on Nei-Gojobori (1986) method and modified Nei-Gojobori (Zhang et al. 1998) method. (Last Update 2010.4.24) [DOWNLOAD]
2. Seq_evolver. This script can generate a random protein-coding sequence, and evolve the sequence into three sequences under a given kappa, omega (dN/dS), and synonymous distance (dS) based on the codon-substitution model by Yang (1998). Omega and synonymous distance can be independently specified for each branch. (Last Update 2010.4.24) [DOWNLOAD]
3. Aln_dna_aa. This script can make a nucleotide based alignment file based on an amino acid sequence alignment obtained by other programs such as ClustalW, MAFFT, and Muscle. (Last Update 2010.4.24) [DOWNLOAD]
4. Distance. This file contains two perl scripts that can compute p-distance and Jukes-Cantor distance for all pairs of sequences with a desired window and sliding sizes. (Last Update 2010.4.24)[DOWNLOAD]
5. Distance_amino_comp. This script can compute p-distance and Poisson Correction distance for all pairs of amino-acid sequences with a desired window and sliding sizes. (Last Update 2010.4.24) [DOWNLOAD]