Mycology and Mushroom Cultivation

Evolution Directory Information exchange among evolutionists

TheScientific World 논문 무료 검색, 원문제공

EMBASE EMBASE.com은 Elsevier Science사에서 의학.약학.생명공학 관련된 "The Excerpta Medica Database : Fullset"를 웹(WEB)을 기반으로 새롭게 출시한 것으로, Biomedeical & Pharmacology와 관련해서는 매우 광범위하고 최신정보를 제공하고, 다른 외부데이터(Medline)나 fulltext 저널과도 연계가 되어 있고, PubMed에 수록되지 않는 유럽 및 기타지역 저널이 많이 추가되어 PubMed 보다도 데이터 량이 훨씬 풍부하고 특히 Drug 관련정보도 훨씬 다양합니다.

Rebase restriction enzyme database

KORSA 학술지 조사 및 원문제공

학술연구정보서비스 학술논문DB는 현재 한국교육학술정보원이 운영하고 있는 국내 최대 학술분야 포털사이트

한국학술정보 국내학회지 PDF원문 이용

KISTI KINITI와 KORDIC 통합기관

KINITI (산업기술정보원)

CABI Commonwealth Agricultural Bureaux International

BIOSIS Life Science의 자료를 모으고 서비스 하는 곳

Laboratory for Conservation Genetics Conservation Genetics Literature Database

랩티즌 과학기술부, 과학재단과 공동으로 산.학.연의 연구활동을 지원하기 위한 커뮤니티 사이트

Human Genome Project 결과

The rRNA WWW Service at Department of biochemistry: Molecular Biology - University of Antwerp (UIA) - BELGIUM

닥터바벤 강원대 환경생물공학부 허원교수, 바이오 벤처기업에 관한 다양한 정보를 제공

Sullivan 시장조사보고서

WIPS 특허검색

KIPRIS 특허검색

IBM Patents 특허검색

USPTO 특허검색

PatentAlert PatentAlert 서비스

Patent Alert/Trade-mark Alert 캐나다 특허 검색 서비스

Patent Search Links 전세계 광범위한 특허 검색 서비스

nowbio

Wiley electronic journal

EcoPort

Medical Information

TradiMed 한국의 전통의학에 대한 데이터베이스

강남기린한방병원

MyDNA 유전자 질환과 치료정보를 제공

Medimail 의사를 위한 의학정보

Pharmail 약사들을 위한 의학정보

Seizure 간질 관련 의학정보

Standup 발기부전 관련 의학정보

Tylenol 두통 관련 의학정보

Footcare 발건강 관련 의학정보

Nizoral 비듬 관련 의학정보

한의학 포털 사이트 한방 뉴스 위주의 의학관련 소식, 전문의를 통한 건강상담

Evolution & Genomics

Bioinformatics

원세연 박사 개인 홈페이지 Bioinformatics에 관한 자료와 많은 link site를 가지고 있음

S-Star 무료 인터넷 생물정보학 강의

Genomics

DOE Microbial genome program

Affimetrix DNA Chip, 기판위에서 직접 oligonucleotide를 합성해가는 방식으로 chip을 만드는 회사

TIGR

Sanger Centre

Caltech Genome Research Laboratory

Genome Sequencing center (중심) of Washington University

Animal Genome Size Database a comprehensive catalogue of published animal genome size data, which is now available online. The database is constantly being updated and is under heavy construction, but already contains C-values for over 2,100 species and subspecies of vertebrates and 800 invertebrates

Sequence and Structure

NCBI

DDBJ (DNA Data Bank of Japan)

EBI (European Bioinformatics Institute)

SWISS-PROT Non-redundant database of protein sequences which contains high-quality annotation and is cross-referenced to many other databases

PDB (Protein Data Bank) Archive of experimentally determined three-dimensional structures of biological macromolecules. The archives contain atomic coordinates, bibliographic citations, primary and secondary structure information, as well as crystallographic structure factors and NMR experimental data

RDP (Ribosomal Database Project II) The Ribosomal Database Project (RDP) provides ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences

TDB (TIGR Database) A collection of curated databases containing DNA and protein sequence, gene expression, cellular role, protein family, and taxonomic data for microbes, plants and humans. Anonymous FTP access to sequence data is also provided

5S rRNA Data Bank Contains 1622 primary structures of 5S rRNAs and 5S rRNA genes from 888 species. DNA or RNA sequences from archaea, eubacteria, plastid, mitochondria and eukaryotes are included

Cloning

VectorDB Contains annotations and sequence information for many vectors commonly used in molecular biology. Information for >2600 vectors, from many different vendors, is available

REBASE (Restriction Enzymes and Methylases) A comprehensive database of information about restriction enzymes and their associated methylases, including their recognition and cleavage sites and their commercial availability. Also included is a listing of homing endonucleases

CUTG (Codon Usage Tabulated from GenBank) Provides codon usage tables for >6000 organisms

Bioinformatics of specific Organisms

Genome Project of Agrobacterium tumefaciens

MIPS The MIPS group (Munich Information center for Protein Sequences of the German National center for Environment and Helath [GSF]) includes a comprehensive database of the yeast genome, a database reflecting the progress in sequencing the Arabidopsis thaliana genome, the systematic analysis of other small genomes, and a collection of protein sequence data

HGMD (Human Gene Mutaiton Database) The Human Gene Mutation Database (HGMD), at the Institute of Medical Genetics in Cardiff, is a collection of known (published) gene lesions responsible for human inherited disease, HGMD provides information of practical importance to researchers and diagnosticians in human molecular genetics, physicians interested in a particular inherited condition, and genetic counselors

EcoCyc (Encyclopedia of Escherichia coli genes and metabolism) A database that combines information about the genome and the intermediary metabolism of E. coli. The database describes 3030 genes of E. coli, 695 metabolic reactions that occur in E. coli, and the organization of these reactions into 123 metabolic pathways. The EcoCyc graphical user interface allows scientists to query and explore the EcoCyc database using scientists to query and explore the EcoCyc database using visualization tools such as genomic-map browsers and automatic layouts of metabolic pathways

CyanoBase Contains genomic information on the cyanobacterium Synechocystis sp. Strain PCC 6803. It provides an annotation for each of the 316B protein genes deduced from the entire nucleotide sequence of this genome. Information on the genome can be directly accessed through three different menus: a clickable physical map of the genome, a gene classification list, and a keyword search menu

Mouse Genome Informatics The overall goal of the Mouse Genome Sequence (MGS) project is to integrate emerging mouse genomic sequence data with the genetic and biological data available in MGD and GXD. MGS is part of the informatics infrastructure needed to support mouse-human comparative genomics.

Mosquito Genomics A collection of both the genetic and physical chromosome mapping data across mosquito species

GOBASE (The Organelle Genome Database Project) The taxonomically broad organelle genome database organizes and integrates diverse data related to organelles (mitochondria and chloroplasts). The current version of GOBASE focuses on the mitochondrial subset of data and contains molecular sequences, RNA secondary structures and genetic maps, as well as taxonomic information for all eukaryotic species represented

Systematics of Organisms

MolSystematics Resource for teaching molecular systematics and evolution

World Taxonomists Database

Softwares

Alex Dong Li's RepeatFinder This is the web interface of Alex Dong Li's repeatfinder version 0.4, to find repeats in a DNA or protein sequence

Bioedit Bioedit is a biological sequence alignment editor written for Windows 95/98/NT. A rich, intuitive multiple document interface with many convenient features makes alignment, manipulation and viewing of sequences relatively quick and easy on your desktop computer. Several sequence manipulation and analysis options and fully-automated links to local and WWW-based anaylsis programs facilitate an integrated working environment which allows you to view, align and analyze sequences from a single application with simple point-and-click operations

Bioinformatics Unit - Weizmann Institute of Science with various softwares

Biomorphs Based on an algorithm described by Richard Dawkins in his book The Blind Watchmaker, "Biomorphs" is a program to demonstrate the potential and the limitations of selection acting on genes and development. The program uses a recursive procedure to "develop" a numerical genotype into an image made of branching and overlapping lines.
The program shows the user a "biomorph" image together with a set of its offspring, differing from the parent by one or a few mutations, and chooses a favorite to become the parent of the next generation. Applying artificial selection, the user can evolve interesting-- and surprisingly lifelike-- "biomorphs."
There is currently no manual to this program, but with a little experimentation it shouldn't be hard to figure out.

Bugs! is a simple genetic algorithm program that simulates bacteria-like organisms which move about in a field of "algae" that they eat by moving over them. When they eat enough of the algae, they reproduce by division; if they don't eat enough, they die. Over time, the initial aimless bugs will evolve into efficient foragers scouring their world for fresh algae.

Circles infers structures using the "comparative method" as opposed to thermodynamic folding. The program is described in the latest issue of Bioinformatics. I also have a short list of secondary structure viewers at this site. If you are using a Windows or Linux, then RnaViz is a very useful tool.

ClustalW & ClustalX Clustal W is a multiple alignment program for DNA and proteins. The program is now more compatible with GCG and has new features for more powerful aligning of diverged sequences

DCSE DCSE (Dedicated Comparative Sequence editor is a multiple alignment edit or. It can be used to edit protein, DNA or RNA alignments. The structure of the molecules can be incorporated in the alignment. It is written in C, and it uses dynamic memory for most things. This means you can almost edit any size of alignment with it. It offers lots of features such as color display of characters and structure, automatic alignment relative to sequences already aligned with others, sequence grouping, sequence or pattern searching, marker system and checking of incorporated RNA structure.

DNA and RNA folding server at Bioinformatics at Rensselaer and the Wadsworth center

Encyclon Neurogenex에서 공개한 web software, DNA sequence analysis, PCR simulator etc.

Game Theory demonstrates the simple Hawk/Dove/Bourgeois game designed to provide an example of the use of game theory in evolutionary theory. Students can adjust payoffs and see the resulting changes in theoretical ESS, and can then check the prediction with both stochastic and analytical simulations. The distribution package includes the program, manual and a sample homework assignment used by Joan Strassmann in her Animal Behavior class, Fall 1996.

GCUA GCUA performs many of the usual codon usage analyses, such as counting codons, analysing base composition etc. It also has a number of multivariate analysis functions and these can be used to analyse the codon and amino acid composition of genomes. The current version is formatted for a maximum of 50,000 genes, enough to analyse the human genome coding regions. These genes can be up to a half a million bases in length. You can also produce a PAUP or PHYLIP - compatible 'distance matrix' based on codon composition (not on pairwise similarities of the sequences).

Genetic Software Forum posting questions and answers regarding
the use of software for genetic analysis

GeneticStudio

Genographer This program will read in data from an ABI 3700, 3100, 377 or 373, CEQ 2000 or SCF and reconstruct them into a gel image which is straightened and sized. Bins can be defined easily and viewed as thumbnails, which allows for a fairly quick and easy way of scoring a gel.

The program is written in Java and uses the Java 1.3 API. Therefore, it should run on any machine that can run java. See Installing and Running for more info.

For a more thourough description of the programs capabilities, see the help files. The tutorial provides a fairly good overview of the program.

This program is distributed under the GNU General Public Liscense.

Goodnight Software contains a lot of softwares including relatedness, Kinships, Game Theory, selection, Sex Ratios, Bugs, Biomorphs, and Is it Chance,

Hickory I am pleased to announce a new release of Hickory, a software package
using Bayesian methods for analysis of geographical structure in genetic
data. The major changes in this release are:

* Analyses of co-dominant marker data with an arbitrary number of
alleles per locus are supported.

* In addition to the GUI version that was distributed last time, we are
including pre-compiled command-line executables that will be useful for
those who need to do large analyses in the background or who want to do
exploratory simulations.

* The documentation has been expanded and describes the use of
Spiegelhalter et al.'s (2002) Deviance Information Criterion as a method
of choosing among alternative models.

* Bayes factor calculations are no longer reported. We were not able to
find a way to make them numerically stable.

We are releasing executables and source code for Hickory under terms of
the GNU General Public License, version 2.0.

Hofacker et al Vienna RNA package A comprehensive package for calculation and analysis of RNA structure. The package includes RNAfold, RNAheat and RNAdraw. RNAdraw. I found RNAdraw very useful to prepare figures for publication as one can save the structure as a windows metafile and edit it using Corel draw.

IBD IBD is a fast, simple and specialized package for Mac and Windows that will analyze 1) raw data from diploid/codominant marker data sets (e.g., allozymes, microsatellites) 2) geographic and genetic distance matrices that have been derived using any methods - Like some other packages, IBD will test for a statistical association between the distance and geographic matrices using a Mantel Test. - IBD will also determine the STRENGTH of this relationship by regressing all pairwise genetic similarity values against their corresponding geographic distances, using Reduced Major axis (RMA) regression. - Confidence intervals for the regression statistics are calculated using a number of different approaches, some of which account for the nonindependence of data points. - Unaltered and log-transformed matrices are both analyzed automatically. - IBD offers several options for dealing with genetic distances that are less than or equal to zero. IBD is available as shareware from: http://www.bio.sdsu.edu/pub/andy/IBD.html The software is documented in: Bohonak, A. J. 2002. IBD (Isolation By Distance): A program for analyses of isolation by distance. Journal of Heredity 93: 154-155. and in a manual available with the download.

Is it chance Does evolution by natural selection propose that complex organs and organisms arose by mere chance? This program pits chance and selection against each other in a race to match a string of random letters to a sentence typed in by the user, and reveals clearly the difference between natural selection and "mere chance."

Kinship is a program to perform maximum likelihood tests of pedigree relationships between pairs of individuals in a population. The program uses genotype information for single-locus, codominant genetic markers (such as DNA microsatellite loci). The user enters two hypothetical pedigree relationships, a primary hypothesis and a null hypothesis, and the program calculates likelihood ratios comparing the two hypotheses for all possible pairs in the data set. The calculation includes a simulation procedure to determine the statistical significance of results. Kinship also calculates pairwise relatedness statistics. The distribution package includes the program, a manual in Microsoft Word 5.1 format, and a sample data set.

LVB LVB is a phylogeny program that searches for parsimonious trees. It is intended for use with very large data matrices (hundreds or thousands of sequences).
A new version is now available for testing. Advantages over the current
release (LVB 1.0A):

- PHYLIP data matrix input format
- Easier to use effectively (fewer parameters to choose)
- Simpler interface
- HTML user manual
- Faster tree evaluation
- Optimized for very large nucleotide data matrices
- Allows ambiguous bases

LVB 2.0 is currently available for Apple MacOS X only. It is a command-line program and must be launched from Terminal (/OsX/Applications/Utilities/Terminal). Please feel free to ask me for advice on this.

A Windows version and source code for Unix/Linux will be made available
later.

MacClade MacClade is a computer program for phylogenetic analysis. Its analytical strength is in studies of character evolution. It also provides many tools for entering and edit (편집)ing data and phylogenies, and for producing tree diagrams and charts.

MEGA2 (Molecular Evolutionary Genetics Analysis software, Version 2.0) Details of statistical and computational methods available in MEGA2 are presented in the book Molecular Evolution and Phylogenetics (M. Nei and S. Kumar, Oxford University Press, 2000; http://www.oup-usa.org/isbn/0195135857.html). This book explains various statistical methods for analyzing molecular data and shows how to interpret the results obtained by various computer programs. It also includes examples of data analysis (see http://lifesciences.asu.edu/mep), a majority of which can be analyzed by MEGA2. Please direct all MEGA related enquiries to Sudhir Kumar (email: bugsr@megasoftware.net)

Mesquite Our knowledge of the characteristics of the world's diverse species (including their DNA sequences) is growing daily. To analyze these data for evolutionary patterns, biologists are relying increasingly on specialized software. A handful of biologist-programmers (ourselves included) have struggled to write and maintain a few massive multi-purpose programs widely used in evolutionary analysis, and many others have written small programs for particular analyses. The inertia of the massive programs and the isolation and idiosyncracies of the small programs have prompted us to develop Mesquite, a new modular system that will allow many programmers to contribute building blocks to a common system. Mesquite began with an emphasis on phylogenetic analysis, but its flexibility allows for other uses in evolutionary biology. It is written in Java™ for ease of development and platform independence

Micro-Checker MICRO-CHECKER is a Windows-based software package for Windows 98 SE, 2000 and XP (not yet tested on NT or ME), which can test the genotyping of microsatellite data from diploid populations. The program aids the identification of various genotyping errors, and can also detect typographic errors. MICRO-CHECKER estimates the frequency of null alleles at a locus using a series of algorithms. Importantly, MICRO-CHECKER can also adjust allele and genotype frequencies of the amplified alleles, which allows the data to be used in further population genetic analysis, for instance with GenePop, Arlequin or Fstat

Microsatellite Analyser

Michael Zuker's pcfold This DOS based program is one of the first to be written. The energy input file can be changed, however this is only recommended for those who have extensive experience is this regard. The output generated is a CT file which can be read by most other secondary structure programs. The output can also be viewed on screen yet the graphic cannot be manipulated and edited in pcfold for publications purposes

Modeltest The use of a model of DNA substitution is routine in the analysis of DNA sequences. Modeltest helps a usert to choose the model of DNA substitution that best fits his/her data among 56 possible models. This is accomplished through an implementation of hierarchical likelihood ratio tests and the AIC criterion.

Morphy

MrBayes MrBayes is a program for Bayesian inference of phylogeny using Markov chain (체인) Monte Carlo methods. MrBayes has a console interface and uses a modified NEXUS format for data and batch files. It handles a wide range of probabilistic models for the evolution of nucleotide and aminoacid sequences, restriction sites, and standard binary data. The user can set the priors used for the parameters and search for trees under topological constraints. The behavior of the Markov chain can be controlled by setting proposal probabilities for different move types and by invoking heated chains (Metropolis Coupling) to improve performance for difficult problems. Various options are available for summarizing the posterior distribution of the model parameters, including topology and branch lengths, and drawing inferences about ancestral states and site rates.

Multilocus analysis of multi-locus population genetic data

Multilocus is a program written to facilitate analysis of multi-locus population genetic data. In particular, it allows calculation of various genotypic diversity indices, linkage disequilibrium indices, masures of population differentiation, and allows one to search for subpopulations which do not share polymorphisms (and thus might be reproductively isolated). It includes a modification of the IA (Index of Association) metric that corrects the scaling effect seen when one applies the metric to different numbers of loci. In addition, there are randomization routines which allow one to test various null hypotheses.
Multilocus is available as Windows and Macintosh (OS X and classic) binaries and as a Unix tarball and has modest disk and memory requirements. Some operations (notably partition searching) may require memory to be significantly increased.

Network2.0c Phylogenetic program package

Oligo Analyzer

Oligomer Calculator This program (for Windows 3.x, runs also under Win9x) allows you to calculate the melting point and concentration for oligonucletides ranging from 14 to 80 bases. You supply the base sequence (and, optionally, absorbance and dilution factor). The program gives the melting temperature (and, optionally, the concentration) of your oligo.

Parente PARENTE is a user-friendly software package that computes parentage inference. Based on the principle of genetic compatibility, PARENTE looks for maternity, paternity or simultaneously for both potential parents, using multilocus genotypes, birth and death dates of individuals (if available). It calculates the probability of successfully allocating an individual
offspring to its parents.

PAUP

PHASE PHASE v1.0. A new version of the computer program PHASE, for reconstructing haplotypes from population genotype data, has been released. It is is free for academic use. The new version incorporates - the ability to deal with missing genotypes - more efficient coding that substantially reduces compute time - a measure of the "goodness of fit" of proposed solutions, allowing results from different runs to be more easily compared. Executables are currently available for Linux and Solaris, and source code is available for those who wish to compile the software on other platforms. It was written by Matthew Stephens (University of Washington, Seattle)

Phydit Seqeunce alignment based on secondary structure and phylogenetic analysis

Phylip PHYLIP is a free package of programs for inferring phylogenies.

Phylogenetic Independence PHYLOGENTIC INDEPENDENCE version 2.0, written by Jeff Reeve and Ehab Abouheif, is now available at: http://ww2.mcgill.ca/biology/faculty/abouheif/index.html

PHYLOGENTIC INDEPENDENCE is a program written to conduct Abouheif's (1999: Evolutionary Ecology Research 1: 895-909) Test For Serial Independence (TFSI) on continuously valued characters and the Runs Test on discretely valued characters.

The TFSI and Runs test are designed to test the assumption of phylogenetic independence within a set of comparative data, i.e., test whether a trait is significantly associated with its phylogenetic history.

It can perform the TFSI and Runs Test using fully or partially resolved phylogenetic trees, and plots the null distribution of the data.

PHYLOGENETIC INDEPENDENCE is available as a Windows PC version or as a command-line version compiled under Red Hat Linux.

Piranah and Grouper These are two macintosh programs that identify conserved RNA pairings by comparative analysis of aligned sequence data. Piranah uses a maximum likelihood algorithm to identify pairings conserved over evolutionary lineages. Grouper can be used on the output of Piranah to assemble the conserved pairings into a secondary structure for the whole molecule. The programs and methods are described in the following reference: Parsch, J., J. M. Braverman, and W. Stephan (2000) Comparative sequence analysis and patterns of covariation in RNA secondary structures. Genetics 154: 909-921.

Rasa This software implements a test and measure of phylogenetic signal called tRASA. It can be used to optimize study design in phylogenetics, to compare signal among genes, to detect long branch sequences, to test available outgroup sequences and to reduce phylogenetic noise. The new version (3.0) is now available as a beta version. Versions older than 3.0 will no longer be supported after 01/31/01

Relatedness calculates average genetic relatedness among sets of individuals defined by demographic variables, either on average or by pairs. It finds standard errors and confidence intervals for signifiance testing using a jackknife resampling method.

RNAStructure Mathews et al 1999 One of the advantages of this program is that you can either fold RNA or DNA. RNA folding is based on the Zuker algorithm and work done by D.H. Mathews, J. Sabina, M. Zuker, and D. H. Turner whereas the DNA folding is based on the folding parameters by J. SantaLucia, Jr "A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics." Proc. Natl. Acad. Sci. USA 95, 1460-1465, (1998)

RnaViz RnaViz is a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings can be created starting from DCSE alignment files if they incorporate structure information or from mfold ct files. The layout of a structure can be changed easily. Display of special structural elements such as pseudo-knots or unformatted areas is possible. Sequences can be automatically numbered, and several other types of labels can be used to annotate particular bases or areas. Although the program does not try to produce an initially non-overlapping drawing, the layout of a properly positioned structure drawing can be applied to newly created drawing using skeleton files. In this way a range of similar structures can be drawn with a minimum of effort. Skeletons for several types of RNA molecule are included with the program

selection is a straightforward population-genetic simulation demonstrating the effects of selection, drift, mutation and migration on allele frequencies in a single-locus, two allele system. The fitnesses of all 3 diploid genotypes can be independently specified, along with population size, mutation rates, migration rate, and the allele frequencies in the external population from which migrants arrive. An onscreen graph shows the results of the simulation. The distribution package includes the program and manual (although this one is straightforward enough you probably won't need the manual).

Sex Ratios is a simple simulation programming for demonstrating Fisherian selection on the sex ratio. The interface is patterned on that of "selection" (above). Users can set the cost of producing male or female offspring, the survivorship of those offspring, the amount each sex will contribute to its own future offspring, and the allocation specified by each of the competing alleles. The simulation then runs to see which of these factors influence selection and the population sex ratio.

SGS The program is called Spatial Genetic Software (SGS). It provides a user- friendly WINDOWS tool to analyse both local and broad scale genetic and phenotypic structure. It can deal with nearly any type of genetic data, codominant (allozyme, PCR-RFLP, microsatellite) or dominant (RAPD, AFLP) markers, biparentally (nuclear) or uniparentally (cpDNA and mtDNA) inherited markers. Data based on any of these markers can be analysed, either as individual genotypes within a single population (local scale) or as allele or haplotype frequencies from different populations (broad scale). We also include a simple approach to analysis of spatial structure for continuous quantitative traits. The program implements various parameters to analyse spatial genetic and phenotypic structure: Moran's index, Geary's index, number of alleles in common, and approaches using genetic distances and FST-values. The statistical significance of all measures is verified by use of a permutation test. The results are assessed by graphics that can be integrated, via the clipboard, to other Windows programs. The details of the computations are given in a table and can be stored in ASCII files. The program has been published recently in the Journal of Heredity: DEGEN, B., PETIT R. and KREMER A. (2001): SGS - Spatial Genetic Software: A computer program for analysis of spatial genetic and phenotypic structures of individuals and populations. Journal of Heredity, 92, 447-448.

Software Link - Crandall Lab link various softwares including MODELTEST, TCS, GEODIS, MATRIX, CHIPERM, PARSPROB, COLLAPSE

Software Link - Felsenstein's Lab

Software Link - Huelsenbeck's Lab

Software Link - PCR Primer Weizmann Institure of Science Genome and Bioinformatics

Splines univariate program for estimating selection functions using the cubic spline

SUNET's, the Swedish University Network's, FTP archive with many softwares

Treefinder There is a more realistic model for protein coding sequences, which is assuming independent rates at the three codon positions. The relative codon position rates can be estimated from the data. Codon position heterogeneity can be combined orthogonally with the usual Gamma heterogeneity and all the substitution models up to the GTR.

TREEFINDER can now perform ML bootstrap analysis to assess the confidence of inferred relationships. As a special feature, it has a consensus routine that is producing trees with edge lengths.

The possibility of specifying topological constraints lets one incorporate ideas about the prior distribution of phylogenetic trees to direct the search.

As usual, the new version is coming with an improved graphical frontend and some minor bug-fixes. The tree viewer is now accepting rooted trees as an input.

TREE-PUZZLE 5.0 TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. It implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch. TREE-PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branch lengths can be calculated under the clock-assumption. In addition, TREE-PUZZLE offers a novel method, likelihood mapping, to investigate the support of a hypothesized internal branch without computing an overall tree and to visualize the phylogenetic content of a sequence alignment. TREE-PUZZLE also conducts a number of statistical tests on the data set (chi-square test for homogeneity of base composition, likelihood ratio clock test, Kishino-Hasegawa test). The models of substitution provided by TREE-PUZZLE are TN, HKY, F84, SH for nucleotides, Dayhoff, JTT, mtREV24, VT, WAG, BLOSUM 62 for amino acids, and F81 for two-state data. Rate heterogeneity is modeled by a discrete Gamma distribution and by allowing invariable sites. The corresponding parameters can be inferred from the data set.

TreeView TreeView is a simple program for displaying phylogenies on Apple Macintosh and Windows PCs

University of Massachusetts, Lowell. Bioinfomatics Web Tools with various web programs for phylogenetics and evolution

Mycology and Mushroom Cultivation

Information Service

사상성진균연구회 국내에서 곰팡이 가지고 일하는데 관심있는 사람들이 만든 연구회, 생물학에 관한 많은 link를 가지고 있음

SYSTEMATIC BOTANY and MYCOLOGY LABORATORY:

월간 버섯

버섯, 영농과 삶

U.S. National Fungus Collections databases We have relied for a long time on the massive databases developed at the US National Fungus Collections. They were among the very first online resources in mycology, have consistently been of the highest quality, and still provide essential tools for mycologists

FunIndex The esteemed mycological group at CABI International (formerly IMI) have compiled a very impressive database of fungal names (variety through family). FunIndex and its related databases include information from the Index of Fungi, Petrak's Lists, the Saccardo Index, Saccardo's Omissions, Zahlbruckner's Catalogue of Lichens, Lamb's Index, the Dictionary of the Fungi classification, and an index to the abstracting journal Bibliography of Systematic Mycology. Whew! The Dictionary of Fungi classification is especially interesting, as it includes a preview of the system to be used in the forthcoming 9th edition

St. Louis Code (in Slovak)

Koeltz Scientific Books

Nomenclatural tutorial

The Phylocode

Stems, nodes, crown clades, and rank-free lists: is Linnaeus dead? By M.J. Benton

The Biocode a proposal that aims to apply a single set of rules to the naming of all organisms

Conserved plant names proposals and disposals

Committee for Fungi

World Taxonomist Database

TRED

Index Herbariorum

IPNI

Aphyllophorales (CBS)

Cortbase (Corticiaceae s.l.)

DERMBASE (Dermateaceae)

Freshwater ascomycetes & anamorphs

Fusarium (CBS)

Xylariaceae

Yeasts (CBS)

Government and Institute

농업과학기술원 연구결과물 게시, 각 부서의 홈은 따로 있음

Company

심전농원 느타리재배기술과 병해충 방제요령, 직거래 장터 및 농장분양

산의농산 (경기도 양평) 느타리버섯 재배에 대한 자료

Fungi Perfecti Mushroom Cultivation에 관계된 사업을 하는 회사

TRAYMASTER (UK) 버섯 생산용 배지 제조, 충진, 폐기물 처리 기계류 제조

ITALSPAWN (Italia) 양송이, 느타리, 표고 등 다양한 버섯 생산

Christiaens Engineering and Construction (Netherland) 버섯 배지용 퇴비 제조기계

JFM (Ireland) & MIS (UK) 버섯 재배사 (터널형), 환기장치, 선반 등 종합 버섯 설비 제조 및 건축

SAS Materials Handling System (Netherland) 버섯 자동 수거 및 수송기

NOOYEN BREE NV (Belgium) 버섯 생산용 배지 공급 (양송이 생산용 퇴비)

Cpoint (Netherland) 버섯 재배 교육기관

MYCOCELL (UK) 버섯 생산용 배지 및 보조제

Fancom (Netherland) 종합 버섯재배 시스템, 기계류

DOFRA BV Horst (Netherland) 버섯 재배용 자동 관수 시스템

장백 밀리타리스 동충하초 농장 동충하초의 종류, 재배법, 활용법, 성분분석 결과 등의 자료 수록

약용자원콜렉션 (공주대 서승염 교수)

동충하초(주)

대한민국 동충하초 (전남 광양시 광양읍 읍내리)

동충하초 (Super Life Net)

진품 누에동충하초 (대한잠업개발공사)

늘푸른 뽕나무농원 상황버섯, 동충하초

임실 동충하초 연구소 굼벵이동충하초 생산

이삭농장 전북 임실, 모준근

Nematology

USDA Nematology Lab

Biocontrol

천적연구 연구결과 및 Biocontrol에 대한 많은 Link를 가지고 있는 곳

USDA Insect Biocontrol Lab in Beltsville Maryland

ARS Biocontrol of Plant Diseases Laboratory

ARS Biocontrol of Plant Diseases Lab

ARS Biocontrol Web Site Gainesville, Florida

ARS Beneficial Insects Introduction Research

ARS European Biological Control Laboratory

APHIS National Biological Control Institute

Biological Control News

APHIS/PPQ Biological Control Programs

APHIS Niles Plant Protection center (중심) Biological Control Programs

North Carolina Department of Agriculture - Biological Control Research and Publications

Industrial Application of Entomopathogenic Fungi from Korea University

Biological Control: A Guide to Natural Enemies in North America from Cornell University

Cornell Community Conference on Biological Control

ESCOP/PMSS Biological Control Working Group

Databases on Noxious Weeds and Insects Wyoming Cooperative Agricultural Pest Survey

FAIRS Florida Agricultural Information Retrieval System.

Biological Control Institute at Auburn University

Landscape Ecology and Biological Control Lab at Michigan State University

Midwest Biological Control News

Purdue Biological Control Laboratory

Nematodes as Biological Control Agents of Insects

Internet Resources on Biological Control from IPMnet's DIR

The Fly In Your Eye an informative and humorous look at CSIRO's fight against the Australian bushfly

International Organization for Biological Control (Nearctic Regional Section)

Consortium for International Crop Protection

Sustainable Agriculture Virtual Library

Association of Natural Bio-control Producers

Bulletin Boards, Questions and Answers from IPMnet

PEST CABWeb CABI Publishing's pest management site

Ooasis

Commercial From the WWW Virtual Library for Agriculture

Beneficial Insectary producer of beneficial insects for biological pest control.

Koppert

March Biological offers beneficial insects, compost systems, and more.

Mycotech offers crop protection products for the agricultural and horticultural markets.

Natural Pest Controls supplier of beneficial insects.

Sierra Ag integrated pest management firm using pheromone mating disruption, lures and traps, beneficial insects, and chemicals to protect various fruits and nuts.

IOBC Working Group on Arthropod Mass Rearing & Quality Control

Association of Natural Bio-Control Producers

Egg Parasitoid News

Association of Natural Bio-control Producers

Suppliers of Beneficial Organisms

IOBC, Arthropod Mass-Rearing and QC

National Biological Control Institute

BioControl News & Information

Midwest Biological Control News

IOBC, SEARS Greenhouse IPM

IOBC, Trichogramma

Cornell Biological Control

Florida National IPM Network

UF Entomology and Nematology Featured Creatures

Florida, DACS, Division of Plant Industry

Florida, DACS, Division of Marketing

Florida Agriculture Census

Agriculture Research Service

UF School of IPM Program

Univ. of California IPM Home Page

North Carolina State BioControl Contents

Label and MSDS data sheets

Nat. Collegiate Inventors & Innovators Alliance

UF Entomology and Nematology Department

UF EDIS (Electronics Document Info System)

University

경북대학교

서울대학교

Lab of Dr. Chun, Jonksik at School of Biological Science, Seoul National University

Duke University Durham, North Carolina

Lab of R. Vilgalys at Department of Biology, Duke University

MacMaster University

Marine Biological Laboratory at Woods Hole, Massachusetts

Josephine Bay Paul center (중심)

Lab of Dr. Jennifer Wernegreen

Michigan State University

Ecology, Evolutionary Biology, and Behavior Program at Michigan State University

Lab of Jeffrey K. Conner at MSU

Lab of Frank B. Dazzo at MSU

Lab of Andrew M. Jarosz at MSU

Lab of Richard E. Lenski at MSU

Lab of Thomas M. Schmidt at MSU

Lab of J Gregory Zeikus at MSU

Ohaio State University Columbus, Ohio

Pennsylvania State University

Rutgers University, The State University of New Jersey

Institure of Marine and Costal Sciences (IMCS)

Santa Clara University at California

Stanford University at California

Technical University of Denmark

University of Arizona at Tucson

Office of International Student Programs and Services

Department of Plant pathology

Lab of Dr. Barry Pryor

University of British Columbia at Vancouver, Canada

Department of Botany, University of Britisch Columbia

Lab of Beverley R. Green at UBC

University of California, Berkeley

Lab of Tom Bruns at UC Berkeley

University of California, Davis

Division of Biological Sciences, UC Davis

The School of Biological Science, The University of Missouri - Kansas City

Lab of Douglas L. Crawford at UMKC. This page is brought to you by Douglas L. Crawford's lab in the Molecular Biology and Biochemistry Division of the School of Biological Sciences at The University of Missouri Kansas City (UMKC). The purpose of this page is to provide a resource for people interested in current research being done in molecular evolution, gene expression, and other related fields.

University of Cincinnati at Cincinnati, Ohio

University of Maryland at Baltimore

University of Maryland Biotechnology Institute at Baltimore

center (중심) of Marine Biotechnology

Lab of Rita R. Colwell

University of Western Ontario

Department of Plant Sciences

Lab of Marc-Andre Lachance

Academic Society

한국미생물학회

한국산업미생물학회

American Society for Microbiology

Britisch Society of Plant Society

Mycological Society of America

Society for Molecular Biology and Evolution

Biotechnology Industry Organization

APS net Plant pathology online

Journal

Cell

Fungal Genetics and Biology

International Journal of Systematics and Evolutionary Microbiology

The Journal of Evolutionary Biology

Molecular Biology and Evolution

Molecular Plant Microbe Interactions

Molecular Plant Pathology

Plant Health Progress

Biotech Company

Amgen

Affimetrix DNA Chip, 기판위에서 직접 oligonucleotide를 합성해가는 방식으로 chip을 만드는 회사

BP 에너지 관련 회사

Applied Molecular Evolution

Diversa

IDEC Pharmaceuticals Pursuing new standards of care in the management of selected cancer and autoimmune diseases

Maxygen Gene shuffle에 대한 원천기술을 보유하고 다양한 효소의 개량을 하고 있는 회사

Nanogen Microelectronics meets molecular biology

Novo Nordisk A/S 산업용 효소의 최대 제조 회사

Reagents and Equipment

Biocarta 생물학관련 시약 및 기구류에 대한 막대한 데이터베이스를 갖추고 있는 사이트

Applied Biosystems ㈜ 랩 써비스 코리아 042-533-1592

Amersham Pharmacia Biotech 비앤비 시스템 042-488-0058

Becton Dickinson Difco media

Biohit 영화과학 02-2140-5400, 042-861-5411

Bioneer

Bio-Rad ㈜비엠에스 02-3471-6500, 042-828-6400

Clontech 코람 바이오텍㈜ 02-556-0311, 042-825-0312

CNBI Calbiochem,Novagen, Novabiochem, Oncogene

Epicentre 엘알에스랩 02-924-8697, 042-828-7711

Eppendorf 고마바이오텍㈜ 02-579-8787

FMC 랩 써비스 코리아 042-533-1592

Invitrogen 고마바이오텍㈜ 02-579-8787

Life Technologies Producer of Gibco BRL Products: ㈜케이디알 02-203-0707, 042-482-1944

Merck Merck Korea Ltd. 02-555-5964

Millipore ㈜삼우트레이딩 02-571-0350

MJ Research

NEB (New England Biolabs ) 코람바이오텍㈜ 042-825-0312

Novagen 엘알에스랩 02-924-8697, 042-828-7711

Pierce 코람바이오텍㈜ 042-825-0312

Promega ㈜랩서비스코리아 042-533-1592

Roche ㈜비엠에스 02-3471-6500, 042-828-6400

Qiagen 엘알에스랩 02-924-8697, 042-828-7711

Sigma-Aldrich Sigma (Biochemicals and reagents for life science research), Aldrich (Organics and inorganics for chemical synthesis), Fluka (Specialty chemicals and analytical reagents for research), Riedel-de Haen (Laboratory chemicals and reagents for research and analysis), Supelco (Chromatography products for analysis and purification): 시그마 알드리치 코리아 02-783-5211, 080-023-7111

Stratagene 코람바이오텍㈜ 042-825-0312

Takara 코아바이오시스템㈜ 02-841-7530, 042-472-3669

Culture Collections

ATCC American Type Culture Collection

CBS Centraalbureau voor Schimmelcultures, Baarn & Delft, The Netherlands

CBS Yeast Database

DSMZ Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (German Collection of Microorganisms and Cell Cultures)

IFO Institute for Fermentation, Osaka

JCM Japan Collection of Microorganisms

KACC 한국 농용미생물 보존센터

KCTC Korean Collection for Type Cultures

NRRL Agricultural Research Service Culture Collection

UKNCC United Kingdom National Culture Collection: Search and order of strains preserved in culture collections such as CCAP, ECACC, NCIMB, NCWRF, CABI, NCTC, NCYC, NCPPB and NCPF