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Biotechnology

Plasmid map / DNA vector drawing software  
Vector map drawing software for simulating DNA cloning plasmid vector experiments allowing for publication of quality graphics.
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MAPMAKER  
MAPMAKER/EXP is a linkage analysis package designed to help construct primary linkage maps of markers segregating in experimental crosses. MAPMAKER/EXP performs full multipoint linkage analysis (simultaneous estimation of all recombination fractions from the primary data) for dominant, recessive, and co- dominant (e.g. RFLP-like) markers.
Submitted: Jan 06, 2001
CompuPed  
The CompuPed genetic database research and pedigree program has an extensive range of capabilities including very fast and correct calculation of Wright's coefficient of inbreeding along with various other genetic inheritance reports that will show you the percentage of total and homozygous genes inherited from each ancestor up to 30 generations back.
Submitted: Nov 17, 2000
Genetic Linkage Analysis  
Four programs included: DISLAMB for single locus linkage disequilibrium analysis for a multiallelic system; DISMULT for multilocus linkage disequilibrium analysis; TDTLIKE for multiallelic likelihood-based version of the TDT test for linkage in pedigree material; MCNMULT for multilocus-multiallelic likelihood-based version of the McNemar test for linkage disequilibrium in pedigree material.
Submitted: Oct 08, 2000
Primer Design Software  
PCR primer design software and oligo tm calculator for real time, nested, cross species, and gmo oligo primer design.
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Advanced Genetics Wizard  
Advanced Genetics Wizard is a free, online program that calculates the genetic makeup of offspring from dominant, codominant and recessive gene crosses.
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Progeny  
Progeny, a unique pedigree drawing program w/built-in transparent relational database providing tremendous flexibility in managing/manipulating data while drawing pedigrees lightning-fast.
Submitted: Oct 20, 2000
GeneBase  
GeneBase is a fully featured user-friendly sequence analysis software, with great emphasis on databasing functions, vector cloning, primer design, professional presentation, and an unparalleled multiple alignment and cluster analysis module. GeneBase combines all the graphical possibilities, ease of use and compatibility of the modern PC-environment with the power and speed of mathematical algorithms developed at Applied Maths.
Submitted: Dec 09, 2000
GCG Wisconsin Package  
Molecular biologists worldwide use the GCG® Wisconsin Package® as their software of choice for comprehensive sequence analysis. The Wisconsin Package meets research needs across disciplines, project teams, and labs to provide an enterprise-wide solution. Based on published algorithms from the fields of mathematical and computational biology, the Package includes tools for: Comparison, Database Searching and Retrieval, DNA/RNA Secondary Structure, Evolution, Fragment Assembly, Gene Finding and Pattern Recognition, Mapping, Primer Selection, and More
Submitted: Dec 10, 2002
LINKAGE  
The core of the LINKAGE package is a series of programs for maximum likelihood estimation of recombination rates, calculation of lod score tables, and analysis of genetic risks. The analysis programs are divided into two groups. The first group can be used for general pedigrees with marker and disease loci. Programs in the second group are for three-generation families and codominant marker loci, and are primarily intended for the construction of genetic maps from data on reference families.
Submitted: Oct 20, 2000
Hands On Genetics  
Hands On Genetics is a company producing computer programs for the teaching and learning of genetics. The programs are intended for the learning of genetics, whether this is done at school or university level, or by private study. They are best used in conjuction with a class or textbook which explains the concepts. The programs test and reinforce the student's knowledge through examples which use these concepts.
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Pedigree Viewer  
The program reads your simple data file and displays the full pedigree structure on the screen. Each animal is represented by its identity, or its name, or by its value for any of the traits in the data file. You can display a large pedigree of thousands of animals all on the screen at the one time. Data are overlapped on the screen for such large pedigrees, but in one mode an individual's information is highlighted as the mouse cursor passes over. You can ask to find an animal(s) by identity, or by merit or merit range for a given trait.
Submitted: Nov 17, 2000
SimLife Scenarios  
SimLife is a commercial application marketed by MindScape which simulates the population dynamics and genetics of an artificial world. The user can define the size of the world and its physical characteristics; temperature level and seasonal fluctuation, amount of water, etc. The organisms which will populate this world can be defined in detail using the 'Biology Lab' module. Having set everything up, the user then populates the world, sets the simulation running and watches what happens.
Submitted: Oct 20, 2000
PedHunter  
PedHunter is a software package that facilitates creation and verification of pedigrees within large genealogies. Linkage analysis requires describing pedigrees for a set of people exhibiting a specific trait and verifying relationships in pedigrees. PedHunter uses methods from graph theory to solve two versions of the pedigree connection problem for genealogies as well as other pedigree analysis problems. The pedigrees are produced by PedHunter as files in LINKAGE format ready for linkage analysis and for drawing with PEDDRAW.
Submitted: Nov 17, 2000
Phylodendron  
An online application for drawing phylogenetic trees, used in evolutionary biology. Options allow you to save in various formats, print, edit, modify, and adorn the tree.
Submitted: Oct 22, 2000
PREPLINK  
WEB-PREPLINK is an alternative to the PREPLINK program which prepares "datafile.dat" for the LINKAGE program. Once finished, the WEB-PREPLINK will display a plain-text version of the datafile.dat on the screen, and the user can save it to a file on his/her local computer.
Submitted: Oct 20, 2000
ArrayDB  
ArrayDB 2.0 is a software suite that provides an interactive user interface for the mining and analysis of microarray gene expression data.
Submitted: Dec 02, 2000
Discovery Studio Gene  
Discovery Studio Gene is the new Accelrys application that brings the legendary ease of use of MacVector™, theaward-winning Macintosh® sequence analysis application, to the Windows platform. DS Gene provides a native Windows® look and feel while retaining the intuitive functionality of its Macintosh counterpart. With DS Gene, you also take advantage of an integrated workbench to organize your sequences and other related files, with a live preview pane that lets you edit, analyze, and align sequences from a single window.
Submitted: Dec 10, 2002
Slink  
Simulation can provide approximate answers to questions that are cumbersome or impossible to answer analytically. For exam- ple, in a linkage study of a disease it is important to know if the pedigrees you have collected (or plan to collect) will be sufficient to detect linkage. The power to detect linkage depends on a variety of factors, such as the structure of the pedigree, the number of affected individuals, and the informativeness of the markers. The SLINK program allows one to carry out such power calculations by simulating genotypes at one locus given the phenotypes at another locus linked with the first locus.
Submitted: Oct 20, 2000
TreeView  
TreeView is a simple program for displaying phylogenies on Apple Macintosh and Windows PCs.
Submitted: Sep 06, 2000
FAST-MAP  
FAST-MAP is a pattern recognition computer program that largely eliminates the key bottleneck currently precluding fully automated genotyping of microsatellite markers -- scoring the alleles. Genetic analysis is useful for localizing genes, diagnosing disease, monitoring cancer, identifying individuals, and assessing genetic risk.
Submitted: Oct 20, 2000
GeneMaths  
GeneMaths is a new high quality software package from Applied Maths, designed for complete analysis of high density microarrays and gene chips. GeneMaths is the only package that combines all applicable mathematical analysis tools with the power of analyzing data sets as large as a million characters per single experiment.
Submitted: Dec 09, 2000
GeneStrut  
GeneStrut is a Macintosh program which computes a range of standard measures for the analysis of genetic structure from discrete genetic data. The input data are multilocus genotypes (typically obtained from enzyme electrophoresis) for individuals sampled from a number of populations, which may be grouped into a hierarchical structure.
Submitted: Oct 15, 2000
PEDPACK  
The package is distributed here primarily for its interactive pedigree graphics capabilities. Included are routines to input the pedigree in Pedpack format, and routines for constructing and improving a graphical representation, for editing the graph interactively, and producing a PostScript output file.
Submitted: Oct 20, 2000
TreeExplorer  
View and manipulate MEGA format trees under Windows.
Submitted: Dec 10, 2000
COMPONENT  
COMPONENT is a computer program for analysing evolutionary trees and is intended for use in studies of phylogeny, tree shape distribution, gene trees/species trees, host-parasite cospeciation, and biogeography.
Submitted: Sep 30, 2000
DNA Microarray Analysis Database Software  
DNA microarray design and analysis software for SNP scoring and cDNA probes. WIN downloadable demos and online ordering are available.
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GeneBio  
GeneBio (Geneva Bioinformatics S.A.) is committed to providing quality databases, software tools and services to the Life Science industry particularly in the field of proteomics.
Submitted: Nov 05, 2000
LOKI  
LOKI_V2.1 is a package developed by Simon C. Heath. LOKI analyses a quantitative trait observed on large pedigrees using Markov chain Monte Carlo multipoint linkage and segregation analysis. The trait may be determined by multiple loci.
Submitted: Oct 20, 2000
Molecular Evolutionary Genetics Anaylsis  
Molecular Evolutionary Genetics Analysis software website. Download software, get information, and communicate with other MEGA2 users.
Submitted: Dec 10, 2000
TagSorter  
TagSorter is a database application designed to simplify the collation, sorting, comparison and identification of SAGE tag sequences. Serial Analysis of Gene Expression (SAGE) is a high through put technique for measuring gene expression profiles (Velculescu et al, 1995). It reveals both the identity of transcripts expressed and their relative abundance. It can also be used as a means of gene discovery.
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VORTEX  
This page provides access to the VORTEX Population Viability Analysis software produced by Bob Lacy.
Submitted: Sep 06, 2000
allgenes.org  
Allgenes.org is a comprehensive gene index or gene catalog that includes genes/transcripts predicted by two largely independent methods: 1. Genes (transcripts) predicted by clustering and assembling EST sequences. 2. Genes predicted by running the ab initio gene finders GRAIL-EXP and GENSCAN on all available human and mouse genomic sequence.
Submitted: Oct 15, 2000
Alta Bioscience  
Oligo synthesis, Oligo peptide synthesis, DNA / gene sequencing, Peptide - Protein sequencing, amino acid analysis, HPLC analysis, MALDI mass spectroscopy.
Submitted: Jan 19, 2001
Bottleneck  
Bottleneck is a program for detecting recent effective population size reductions from allele data frequencies.
Submitted: Oct 08, 2000
Cyrillic  
Pedigree drawing with fully integrated risk analysis and support for industry standard databases.
Submitted: Nov 17, 2000
GEMMA  
GEMMA developped with 4D (ACI) is running on Macintosh and devoted to the management of genotyping laboratories. GEMMA allows to manage animals, pedigree, DNA samples, markers, PCR protocols, primers , alleles, gel and PCR 96-well sample sheets, genotypes and phenotypes, dossiers, sets of markers and animals, genetic distance and more.
Submitted: Nov 16, 2000
Karl Broman's Software  
RelCheck - Software for verifying relationships between all pairs of individuals in a linkage study, using the approach of Boehnke and Cox. f2 - Software for QTL analysis of an F2 intercross experiment, including forward selection for multiple QTLs, all pairs of loci, and pairwise interactions.
Submitted: Sep 19, 2000
LabCollector  
Molecular Biology lab information management software. The main concept behind LabCollector is that each scientist in the lab can manage quickly his data and make them available to the rest of the lab community. Due to Intranet support, data can be accessed from any connected computer in the lab, which accelerates information retrieval.
Submitted: Mar 10, 2003
Mavric  
Mavric is a python module for the manipulation and visualization of phylogenetic trees. It is also a recursive acronym for Mavric Visualizes Rick's Cladograms :) It aims to be a user-friendly tool for manipulating phylogenetic trees on *NIX-like systems, especially Linux. As such it complements other phylogeny programs like those in the PHYLIP package, which for all their strengths currently lack a nice graphical interface.
Submitted: Oct 15, 2000
Seaview  
This is a graphical editor to deal with biosequences. SeaView is able to read various alignment formats (MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows ones to manually edit the alignment, and also to run ClustalW to locally improve the alignment.
Submitted: Jan 06, 2001
123D+  
123D+ is a program which combines substitution matrix, secondary structure prediction, and contact capacity potentials to thread a sequence throught the set of structures.
Submitted: Dec 10, 2000
Jarnac  
Jarnac is a language for describing and manipulating cellular system models and can be used to describe metabolic, signal transduction and gene networks, or in fact any physical system which can be described in terms of a network and associated flows.
Submitted: Sep 30, 2000
TreeRot.v2  
TreeRot is a Macintosh program that aids in the determination of decay or Bremer support indices (Bremer 1988) by generating a command file for PAUP or PAUP* (Swofford 1993, 1999). The command file includes 1) a constraint statement for each node in a given shortest or strict consensus tree and 2) commands to search for trees inconsistent with each of these constraint statements in turn.
Submitted: Oct 15, 2000
TYPENEXT  
TYPENEXT is an application of computer simulation which can assist an investigator in selecting which untyped individuals in a pedigree would contribute most to the expected lod score if they were to be typed.
Submitted: Oct 20, 2000
VaryPhen  
The VaryPhen program is a utility program, which may be used as a tool in linkage analysis.
Submitted: Oct 20, 2000
VITESSE  
VITESSE is a software package that computes likelihoods with the functionality of the LINKMAP and MLINK programs from LINKAGE. VITESSE uses the novel algorithms of set-recoding and fuzzy inheritance to reduce the number of genotypes needed for exact computation of the likelihood, which accelerates the calculation. It also represents multilocus genotypes locus-by-locus to reduce the memory requirements.
Submitted: Oct 20, 2000



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