Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== NAME K-Estimator 4.3 DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Molecular Evolution DESCRIPTION K-Estimator is a computer program for estimating the number DESCRIPTION of nucleotide substitutions per site (synonymous, Ks, and DESCRIPTION nonsynonymous, Ka, for coding regions, and overall, K, for DESCRIPTION noncoding regions) and the confidence intervals of these DESCRIPTION estimates obtained by Monte-Carlo simulations. For DESCRIPTION noncoding regions, K can be estimated by applying several DESCRIPTION methods to correct for multiple-hits (Jukes and Cantor, DESCRIPTION Kimura-2p, Tajima and Nei, Tajima 1-, 2-, and 3-p). For DESCRIPTION coding regions Ks and Ka are estimated based on the method DESCRIPTION described in Comeron (1995). AUTHOR Josep M. Comeron RA Comeron, J.M.; RT "A method for estimating the numbers of synonymous RT and nonsynonymous substitutions per site"; RL J. Mol. Evol. 41:1152-1159(1995). ADDRESS Dep. Ecology and Evolution ADDRESS University of Chicago ADDRESS 1101 east 57th St. ADDRESS Chicago, IL 60637, USA CONTACT jcomeron@midway.uchicago.edu SITE WWW Server at URL http://mk-dimension-1.uchicago.edu OS PC LANGUAGE Visual Basic 5 VOLUME 3 Mb REQUIRES Windows 95/98/NT AC BC00588 NAME DAMBE (Data analysis in molecular biology and evolution) DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Alignment editing and display DOMAIN Alignment browser DOMAIN Genetic tools DOMAIN Molecular Evolution DOMAIN Phylogeny DOMAIN Database and analysis DOMAIN Searching databases DOMAIN General tools DOMAIN Statistical significance DOMAIN Comparative analysis DESCRIPTION DAMBE (Data Analysis in Molecular Biology DESCRIPTION and Evolution) is an integrated software package for DESCRIPTION converting, manipulating, statistically and graphically DESCRIPTION describing and analyzing molecular sequence data, with a DESCRIPTION user-friendly Windows 95 interface. AUTHOR Xuhua Xia RT - ADDRESS Department of Ecology & Biodiversity, ADDRESS University of Hong Kong, Hong Kong CONTACT xxia@hkusua.hku.hk SITE WWW Server at URL http://web.hku.hk/~xxia/software/software.htm OS Windows 95 LANGUAGE - VOLUME 10 MB REQUIRES Windows 95 AC BC00591 NAME K-Estimator 5.0 DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Molecular Evolution DESCRIPTION K-Estimator is a computer program for estimating the number DESCRIPTION of nucleotide substitutions per site (synonymous [Ks], and DESCRIPTION nonsynonymous [Ka], for coding regions, and overall [K], for DESCRIPTION noncoding regions) and the confidence intervals of these DESCRIPTION estimates obtained by Monte-Carlo simulations. DESCRIPTION Divergence Estimates: For noncoding regions, the program can DESCRIPTION estimate the overall (K) number of nucleotide substitutions DESCRIPTION per site using several multiple-hits at a site correcting DESCRIPTION methods: Jukes and Cantorīs 1-parameter (Jukes and Cantor, 1969), DESCRIPTION Kimuraīs 2-p(Kimura, 1980), Tajima and Nei (Tajima and Nei, 1984), DESCRIPTION and Tajimaīs 1-p, 2-p and 4-p (Tajima, 1993). DESCRIPTION When coding regions are under analysis, K-Estimator 5.0 applies DESCRIPTION the method described in Comeron (1995) to estimate Ks and Ka. DESCRIPTION This method is a modification of Li's (1993) and Pamilo and DESCRIPTION Bianchi's (1993)(LPB) method that better quantifies the actual DESCRIPTION number of transitions and transversions and reduces stochastic DESCRIPTION errors (see Comeron, 1995, for details and comparison to previous DESCRIPTION methods). Three genetic codes can be applied: Universal, DESCRIPTION Vertebrate mitochondrial, or Drosophila mitochondrial. DESCRIPTION Furthermore, three different options can be applied to restrict DESCRIPTION the codons that are under analysis. DESCRIPTION Confidence Intervals: K-Estimator 5.0 obtains the Confidence DESCRIPTION Intervals (C.I.) of divergence estimates (K for noncoding regions, DESCRIPTION and Ks and Ka for coding regions) by Monte Carlo simulations. DESCRIPTION Computer simulations take into account the following parameters: DESCRIPTION 1)Divergence Value; K or Ks and Ka, 2)number of nucleotides or DESCRIPTION codons, 3)the transition : transversion (alfa:beta) substitution DESCRIPTION ratio, and 4) the G+C content for noncoding regions, and the DESCRIPTION amino acid composition and G+C content at the third position of DESCRIPTION codons for coding regions. The program can also calculate the DESCRIPTION exact probability of obtaining any particular divergence value DESCRIPTION (K for noncoding regions, and Ks, Ka, and Ka/Ks for coding DESCRIPTION regions). DESCRIPTION K-Estimator 5.0 also obtain the expected distribution of the ratio DESCRIPTION Ka/Ks that has been classically applied to detect the action of DESCRIPTION positive selection (Ka/Ks>1). In particular, the program generates DESCRIPTION a condition where the number of nonsynonymous substitutions per DESCRIPTION nonsynonymous site (Ka) is on average equal to the value estimated DESCRIPTION for Ks, taking into account all the previous parameters from the DESCRIPTION analyzed pair of sequences. Therefore, it is obtained the null DESCRIPTION distribution and C.I. for Ks, Ka and, more important, for the DESCRIPTION ratio Ka/Ks, when the expectation (null hypothesis) for Ka/Ks is =1. AUTHOR Josep M. Comeron RA Comeron, J.M.; RT "A method for estimating the numbers of synonymous and RT nonsynonymous substitutions per site"; RL J. Mol. Evol. 41:1152-1159(1995). RA Comeron, J.M.; RT "K-Estimator: Calculation of the number of nucleotide RT substitutions per site and the confidence intervals"; RL Bioinformatics (1999, in press). ADDRESS Dep. Ecology and Evolution ADDRESS University of Chicago ADDRESS 1101 east 57th St. ADDRESS Chicago, IL 60637, USA CONTACT jcomeron@midway.uchicago.edu SITE WWW Server at URL http://mk-dimension-1.uchicago.edu OS PC LANGUAGE Visual Basic 5 VOLUME 3 Mb REQUIRES Windows 98/NT AC BC00596 NAME SimPlot DOMAIN Sequence analysis DOMAIN Protein sequence analysis DOMAIN Molecular Evolution DOMAIN Statistical significance DESCRIPTION SimPlot is a graphical program for analysis of sequences DESCRIPTION (e.g. HIV) suspected of being recombinant. The program DESCRIPTION recognizes multiple file formats, and sequences can be DESCRIPTION analyzed individually or as members of groups. Three DESCRIPTION major methods are available: similarity/diversity plots, DESCRIPTION bootscanning, and informative site analysis. Results DESCRIPTION can be printed, copied to the Windows clipboard, or DESCRIPTION saved as a graphics metafile. The author reserves DESCRIPTION copyright, but the software is provided at no cost. AUTHOR Stuart C. Ray, M.D. RA Lole K.S., Bollinger R.C., Paranjape R.S., Gadkari D., RA Kulkarni S.S., Novak N.G., Ingersoll R., Sheppard H.W., and Ray S.C.; RT "Full-Length Human Immunodeficiency Virus Type 1 Genomes RT from Subtype C-Infected Seroconverters in India, with RT Evidence of Intersubtype Recombination"; RL J Virol 73:152-160 (1999). ADDRESS Stuart C. Ray, M.D. ADDRESS Division of Infectious Diseases ADDRESS Johns Hopkins University School of Medicine ADDRESS 720 Rutland Avenue, Ross 1159 ADDRESS Baltimore, MD 21205 CONTACT sray@jhmi.edu SITE WWW Server at URL http://www.med.jhu.edu/deptmed/sray/download/ OS Windows 95, Windows 98, Windows NT LANGUAGE Pascal (Borland Delphi) VOLUME 1.2 MB REQUIRES 32-bit PHYLIP (phylip95.exe)