Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== AC BC00500 NAME DnaSP DOMAIN Sequence format conversion tools DOMAIN Sequence analysis DOMAIN Sequence tools DOMAIN Population Genetics DESCRIPTION DnaSP is a software package for Windows that DESCRIPTION performs extensive population genetics analyses on DNA DESCRIPTION sequence data. DESCRIPTION DnaSP estimates several measures of DNA sequence DESCRIPTION polymorphism within and between populations (in noncoding, DESCRIPTION synonymous or nonsynonymous sites), linkage disequilibrium, DESCRIPTION recombination, gene flow, and gene conversion. DESCRIPTION The program can also perform the analysis of the pairwise DESCRIPTION differences distribution (mismatch distribution), and the DESCRIPTION frequency spectrum in constant size and in growing populations. DESCRIPTION DnaSP can also conduct some neutrality tests: Fu and DESCRIPTION Li's; Hudson, Kreitman and Aguade; McDonald and Kreitman; DESCRIPTION and Tajima's tests. DESCRIPTION DnaSP can estimate the confidence intervals of some test- DESCRIPTION statistics by the coalescent. DESCRIPTION DnaSP allows performing several analyses by the sliding window DESCRIPTION method, and also to obtain graphic representations. DESCRIPTION Input: Aligned DNA sequences in NBRF/PIR, MEGA, PHYLIP and NEXUS DESCRIPTION file formats. DESCRIPTION Output: the results are displayed in tables and graphs. The DESCRIPTION output can be either sent to the printer or saved in a file. DESCRIPTION The program can handle a large number of sequences (hundreds) DESCRIPTION of thousands of nucleotides each. AUTHOR Julio Rozas and Ricardo Rozas RT "DnaSP version 3: an integrated program for molecular population RT genetics and molecular evolution analysis" RL Bioinformatics 15: 174-175 (1999). ADDRESS Departament de Genetica ADDRESS Facultat de Biologia ADDRESS Universitat de Barcelona ADDRESS Diagonal 645 ADDRESS Barcelona 08071 ADDRESS Spain ADDRESS Phone: +34 93-4021495 ADDRESS Fax: +34 93-4110969 CONTACT julio@porthos.bio.ub.es SITE WWW Server at URL http://www.bio.ub.es/~julio/DnaSP.html SITE ftp anonymous ftp.ebi.ac.uk SITE Directory /pub/software/dos/dnasp SITE-CONTACT nethelp@ebi.ac.uk SITE DnaSP updates: SITE WWW Server at URL http://www.bio.ub.es/~julio/DnaSP.html OS Winodws 95, 98, NT LANGUAGE Visual Basic 5.0 VOLUME 3992 Kb REQUIRES PC Pentium, 16 Mb RAM COMMENTS For academic uses, DnaSP is available free of charge AC BC00512 NAME GEPASI DOMAIN Population Genetics DOMAIN Metabolic regulation DESCRIPTION Gepasi is intended for the simulation of the DESCRIPTION kinetics of systems of chemical and biochemical reactions. DESCRIPTION Gepasi is able to simulate the steady-state and time DESCRIPTION course behaviour of reactions in several compartments of DESCRIPTION different volumes. The user supplies the program with DESCRIPTION information about the stoichiometric structure of the DESCRIPTION pathway, kinetics of each reaction, volumes of the DESCRIPTION compartments and initial concentration of the chemical DESCRIPTION species. The program then builds the implicit differential DESCRIPTION equations and solves them, both for steady state and time DESCRIPTION course. Results can be plotted in 2D and 3D graphs directly DESCRIPTION from the program (by using gnuplot, included here). Steady DESCRIPTION states are analysed with metabolic control analysis (MCA) DESCRIPTION and linear stability analysis (eigenvalues of the DESCRIPTION Jacobian). Data is output in ASCII columnar files that can DESCRIPTION easily be loaded in other programs. AUTHOR Pedro Mendes RA Mendes, P.; RT "GEPASI: a software package for modelling the dynamics, RT steady states and control of biochemical and other systems."; RL Comput. Appl. Biosci. 9:563-571(1993). ADDRESS Institute of Biological Sciences ADDRESS Edward Llwyd Building ADDRESS University of Wales ADDRESS Aberystwyth ADDRESS Ceredigion SY23 3DA ADDRESS United Kingdom CONTACT prm@aber.ac.uk SITE WWW Server at URL http://gepasi.dbs.aber.ac.uk/softw/gepasi.html OS Windows 95, Windows NT LANGUAGE - VOLUME 3 Mb REQUIRES - AC BC00515 NAME DROSOPOSON DOMAIN Genetic tools DOMAIN Population Genetics DOMAIN Database and analysis DOMAIN Statistical significance DOMAIN Comparative analysis DESCRIPTION An object-oriented knowledge base dedicated DESCRIPTION on localisation data of transposable element insertions DESCRIPTION along the polytene chromosomes of Drosophila. The base DESCRIPTION brings together: DESCRIPTION 1) data available on chromosomal localisations of DESCRIPTION transposable element insertions and on features of the DESCRIPTION polytene chromosomes (DNA content, recombination rate, DESCRIPTION breakpoints...), 2) some statistical methods aimed at DESCRIPTION analysing the distribution of the transposable element DESCRIPTION insertions along the chromosomes, in relation with the DESCRIPTION chromosome features. DROSOPOSON can thus be used either as DESCRIPTION a consultation tool, as an instant look of the available DESCRIPTION knowledge, or to analyse user's data. AUTHOR Christine HOOGLAND RA Hoogland C., Biemont C.; RT "DROSOPOSON: a knowledge base on chromosomal localization of RT transposable element insertions in Drosophila."; RL Compu. Appl. Biosci. 13:61-68(1997). ADDRESS Laboratoire de Biometrie, Genetique et Biologie des populations ADDRESS UMR CNRS 5558 ADDRESS Universite C. Bernard - Lyon 1 ADDRESS 69622 Villeurbanne ADDRESS France CONTACT hoogland@biomserv.univ-lyon1.fr SITE ftp anonymous biom3.univ-lyon1.fr SITE Directory /pub/drosoposon SITE-CONTACT - OS Sun/Solaris LANGUAGE LE_LISP VOLUME - REQUIRES - COMMENTS Commercial softwares needed: Le_Lisp and Aida by ILOG (ILOG SA, Gentilly, France); COMMENTS Knowledge base manager: SHIRKA developed by INRIA and the ARTEMIS laboratory in Grenoble, COMMENTS France (Francois.Rechenmann@inria.fr). COMMENTS All the files (data, programs, schemes) are available independently, as plain text. AC BC00525 NAME TFPGA (Tools for population genetic analyses) DOMAIN Population Genetics DESCRIPTION TFPGA is a windows program for the analysis DESCRIPTION of allozyme and molecular population genetic data. The DESCRIPTION program calculates simple descriptive statistics, genetic DESCRIPTION distances, and F-statistics. It also performs tests for DESCRIPTION Hardy-Weinberg equilibrium, population differentiation and DESCRIPTION performs UPGMA clustering and Mantel Tests. AUTHOR Miller, Mark P. RT - ADDRESS Department of Biological Sciences - Box 5640 ADDRESS Northern Arizona University ADDRESS Flagstaff, AZ 86011-5640 CONTACT mpm2@nauvax.ucc.nau.edu SITE WWW Server at URL http://dana.ucc.nau.edu/~mpm2 OS Microsoft Windows LANGUAGE - VOLUME - REQUIRES - AC BC00540 NAME Migrate DOMAIN Population Genetics DESCRIPTION Migrate is a maximum likelihood estimator DESCRIPTION for migration rates and effective population sizes using an DESCRIPTION extension of coalescence theory. The current version uses a DESCRIPTION simple two population model with 4 parameters: population DESCRIPTION sizes for each subpopulation and migration rates for each DESCRIPTION subpopulation. Data from several loci can be combined DESCRIPTION either by assuming the mutation rate is constant between DESCRIPTION loci, or that the mutation rate is following a Gamma DESCRIPTION distribution. Input data can be either sequence data, DESCRIPTION microsatellite data, or enzyme electrophoretic data. AUTHOR Peter Beerli, Joseph Felsenstein RT - ADDRESS Dr. Peter Beerli ADDRESS Genetics 357360 ADDRESS University of Washington ADDRESS Seattle WA 98195 ADDRESS USA CONTACT beerli@genetics.washington.edu SITE WWW Server at URL http://evolution.genetics.washington.edu/lamarc.html OS Source, Linux, NeXT, DUNIX (Alpha), Powermac, Windows95/NT LANGUAGE C VOLUME <2MB REQUIRES - COMMENTS Migrate is part of a loose package named LAMARC AC BC00544 NAME Bottleneck DOMAIN Population Genetics DESCRIPTION Bottleneck is a program for detecting recent effective DESCRIPTION population size reductions from allele data frequencies. AUTHOR Piry S., Cornuet J.M., Luikart G. RA Cornuet J.M. and Luikart G.; RT "Description and power analysis of two tests for RT detecting recent population bottlenecks from allele RT frequency data."; RL Genetics 144:2001-2014 (1997). ADDRESS Laboratoire de Modélisation et de Biologie Evolutive ADDRESS INRA-URLB ADDRESS 488 rue de la Croix-Lavit ADDRESS F-34090 Montpellier ADDRESS FRANCE CONTACT piry@ensam.inra.fr SITE WWW Server at URL http://www.ensam.inra.fr/~piry OS Windows95 LANGUAGE Delphi 2.0 VOLUME < 1Mo REQUIRES Pentium, Windows95 COMMENTS Graphical User Interface COMMENTS Read Genepop and Genetix data files AC BC00584 NAME Recombine DOMAIN Population Genetics DESCRIPTION RECOMBINE estimates the effective population size and per-site DESCRIPTION recombination rate of a single constant-size population. DESCRIPTION RECOMBINE fits a model which has a single population of DESCRIPTION constant size with a single recombination rate across all DESCRIPTION sites. It can accomodate eitherplain DNA or RNA data or DESCRIPTION SNP (Single Nucleotide Polymorphism)data. It estimates DESCRIPTION 4Nu and r, where N is the effective population size, DESCRIPTION u is the neutral mutation rate per site, DESCRIPTION and r is the ratio of the per-site recombination rate to DESCRIPTION the per-site mutation rate. DESCRIPTION If you have a PowerMac, you will want to fetch the PowerMac DESCRIPTION binary; or if you have an Intel processor with Windows95 or DESCRIPTION Windows NT you want the file finstall.exe. AUTHOR Mary K. Kuhner RT - ADDRESS Department of Genetics SK-50 ADDRESS J255 Health Sciences ADDRESS University of Washington ADDRESS Seattle, WA 98115, USA CONTACT mkkuhner@genetics.washington.edu SITE WWW Server at URL http://evolution.genetics.washington.edu/lamarc/recombine.html OS PowerMac, Windows95/NT, DecULTRIX and UNIX, SGI, Solaris LANGUAGE C VOLUME - REQUIRES gcc to compile on Solaris COMMENTS Download source or binary (for PowerMacs or Windows95/NT[Intel]) and documentation. The source COMMENTS code will compile with any recent C-compiler (successfully compiled on DEC ULTRIX, DEC alpha, COMMENTS Powermac, INTEL machines, NeXT, SGI; needs gcc to compile on Suns). COMMENTS Recombine is part of a loose package named LAMARC AC BC00585 NAME Fluctuate DOMAIN Population Genetics DESCRIPTION FLUCTUATE fits the model which has a single population DESCRIPTION which has been growing (or shrinking) according to an DESCRIPTION exponential growth law. It estimates 4Nu and g, where N DESCRIPTION is the effective population size, u is the neutral DESCRIPTION mutation rate per site, and g is the growth rate of DESCRIPTION the population. AUTHOR Mary K. Kuhner RT - ADDRESS Department of Genetics SK-50 ADDRESS J255 Health Sciences ADDRESS University of Washington ADDRESS Seattle, WA 98115, USA CONTACT mkkuhner@genetics.washington.edu SITE WWW Server at URL http://evolution.genetics.washington.edu/lamarc/fluctuate.html OS PowerMac, Windows95/NT, DEC ULTRIX and UNIX, SGI, Solaris LANGUAGE C VOLUME - REQUIRES gcc to compile on Solaris COMMENTS If you have a PowerMac, you will want to fetch the PowerMac COMMENTS binary, or if you have an Intel processor with Windows95 or COMMENTS Windows NT you want the file finstall.exe. COMMENTS Download source or binary (for PowerMacs or Windows95/NT[Intel]) COMMENTS and documentation. The source code will compile with any COMMENTS recent C-compiler (successfully compiled on DEC ULTRIX, COMMENTS DEC alpha, Powermac, INTEL machines, NeXT, SGI; COMMENTS needs gcc to compile on Suns). COMMENTS Fluctuate is part of a loose package named LAMARC