基于DNA分子标记数据构建系统进化树的新策略

结合DPS软件和MEGA软件优点,进行DNA分子标记数据处理和系统发育树构建的新策略：首先使用DPS软件进行0,1数据系统聚类方法获得遗传距离矩阵,然后将此矩阵输入MEGA3,利用NJ或者UPGMA进行系统进化树的构建和树的优化。该方法操作简单,得到的树形美观。     

An index of substitution saturation and its application

We introduce a new index to measure substitution saturation in a set of aligned nucleotide sequences. The index is based on the notion of entropy in information theory. We derive the critical values of the index based on computer simulation with different sequence lengths, different number of OTUs and different topologies. The critical value enables researchers to quickly judge whether a set of aligned sequences is useful in phylogenetics. We illustrate the index by applying it to an analysis of the aligned sequences of the elongation factor-1alpha gene originally used to resolve the deep phylogeny of major arthropod groups. The method has been implemented in DAMBE.     

Software tools and databases for bacterial systematics and their disseminationvia global networks

The dynamic expansion of the taxonomic knowledge base is fundamental to further developments in biotechnology and sustainable conservation strategies. The vast array of software tools for numerical taxonomy and probabilistic identification, in conjunction with automated systems for data generation are allowing the construction of large computerised strain databases. New techniques available for the generation of chemical and molecular data, associated with new software tools for data analysis, are leading to a quantum leap in bacterial systematics. The easy exchange of data through an interactive and highly distributed global computer network, such as the Internet, is facilitating the dissemination of taxonomic data. Relevant information for comparative sequence analysis, ribotyping, protein and DNA electrophoretic pattern analysis is available on-line through computerised networks. Several software packages are available for the analysis of molecular data. Nomenclatural and taxonomic Authority Files are available from different sources together with strain specific information. The increasing availability of public domain software, is leading to the establishment and integration of public domain databases all over the world, and promoting co-operative research projects on a scale never seen before.     

BALL--rapid software prototyping in computational molecular biology. Biochemicals Algorithms Library

MOTIVATION: Rapid software prototyping can significantly reduce development times in the field of computational molecular biology and molecular modeling. Biochemical Algorithms Library (BALL) is an application framework in C++ that has been specifically designed for this purpose. RESULTS: BALL provides an extensive set of data structures as well as classes for molecular mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization. BALL has been carefully designed to be robust, easy to use, and open to extensions. Especially its extensibility which results from an object-oriented and generic programming approach distinguishes it from other software packages. BALL is well suited to serve as a public repository for reliable data structures and algorithms. We show in an example that the implementation of complex methods is greatly simplified when using the data structures and functionality provided by BALL.     

Genotype transposer: automated genotype manipulation for linkage disequilibrium analysis

SUMMARY: The purpose of this work is to provide the modern molecular geneticist with tools to perform more efficient and more accurate analysis of the genotype data they produce. By using Microsoft Excel macros written in Visual Basic, we can translate genotype data into a form readable by the versatile software 'Arlequin', read the Arlequin output, calculate statistics of linkage disequilibrium, and put the results in a format for viewing with the software 'GOLD'. AVAILABILITY: The software is available by FTP at: ftp://xcsg.iarc.fr/cox/Genotype_Transposer/. SUPPLEMENTARY INFORMATION: Detailed instruction and examples are available at: ftp://xcsg.iarc.fr/cox/Genotype&_Transposer/. Arlequin is available at: http://lgb.unige.ch/arlequin/. GOLD is available at: http://www.well.ox.ac.uk/asthma/GOLD/.     

BioPAX support in CellDesigner

MOTIVATION: BioPAX is a standard language for representing and exchanging models of biological processes at the molecular and cellular levels. It is widely used by different pathway databases and genomics data analysis software. Currently, the primary source of BioPAX data is direct exports from the curated pathway databases. It is still uncommon for wet-lab biologists to share and exchange pathway knowledge using BioPAX. Instead, pathways are usually represented as informal diagrams in the literature. In order to encourage formal representation of pathways, we describe a software package that allows users to create pathway diagrams using CellDesigner, a user-friendly graphical pathway-editing tool and save the pathway data in BioPAX Level 3 format. AVAILABILITY: The plug-in is freely available and can be downloaded at ftp://ftp.pantherdb.org/CellDesigner/plugins/BioPAX/ CONTACT: huaiyumi@usc.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

DetSel 1.0: a computer program to detect markers responding to selection

Estimating population parameters from polymorphism frequency data requires neutral genetic markers. Any departure from neutrality may invalidate the inferences drawn from such analyses. We recently discussed the possibility of identifying markers that show deviation from neutral expectations in pairwise comparisons of diverging populations. We are now releasing a user-friendly software package that implements all the necessary steps to identify the signature of selection among molecular markers in a set of polymorphism data. This software can be downloaded free of charge at http://www.univ-montp2.fr/~genetix/detsel/detsel.html.     

The Nucleic Acid Blot Analyzer II. ANALYZE, an image analysis software package for molecular biology

The Nucleic Acid Blot Analyzer, a new instrument providing high-speed imaging of 32P labeled nucleic acids, captures, stores and presents images in digital form, thus lending itself to rapid data handling and analysis as well as replacing conventional X-ray film autoradiography for many applications. A software package called ANALYZE has been specifically designed for the instrument in order to provide automatic or semi-automatic analysis for molecular biological techniques. The software includes image display manipulation, quantitative and positional analysis, as well as file maintenance utilities. The specific application of the software/hardware to various techniques is presented.     

PGEToolbox: A Matlab toolbox for population genetics and evolution

Assessing genetic diversity within populations is vital for understanding the nature of evolutionary processes at the molecular level. PGEToolbox is a Matlab-based open-sourced software package for data analysis in population genetics. The main features of this software are as follows: 1) capability for handling both DNA sequence polymorphisms and single nucleotide polymorphisms (SNPs), which include genotype and haplotype data; 2) exhaustive population genetic analyses and neutrality tests based on the coalescent theory; 3) extendibility and scalability for complex and large genome-wide datasets; 4) simple yet effective graphic user interfaces and sophisticated visualization of data and results. For academic uses, PGEToolbox is available free of charge at http://bioinformatics.org/pgetoolbox.     

Survival analysis tools in genomics research

There is an increasing demand to determine the clinical implication of experimental findings in molecular biomedical research. Survival (or failure time) analysis methodologies have been adapted to the analysis of genomics data to link molecular information with clinical outcomes of interest. Genome-wide molecular profiles have served as sources for discovery of predictive/prognostic biomarkers as well as therapeutic targets in the past decade. In this review, we overview currently available software, web applications, and databases specifically developed for survival analysis in genomics research and discuss issues in assessing clinical utility of molecular features derived from genomic profiling.     

Vector NTI Suite在分子生物学领域的应用

有许多软件可以帮助分子生物学工作者解决一些他们日常实验室工作中遇到的问题.Vector NTI Suite是一种高度集成、功能齐全的分子生物学应用软件,它可以对核酸、蛋白质等分子进行大量的操作和分析,以及建立和管理生物数据库.重点对Vector NTI Suite软件的概况、应用现状及其在分子生物学领域的应用进行综述与探讨.     

LDA--a java-based linkage disequilibrium analyzer

SUMMARY: We describe an integrated java-based program that provides elaborate graphic and plain-text output of pairwise linkage disequilibrium (LD) analysis of single nucleotide polymorphisms genotypic data. It is most suitable for molecular geneticists, who are focusing on LD measures estimation, statistical significance test and extent prediction. AVAILABILITY: The software is available at: http://www.chgb.org.cn/lda/lda.htm. SUPPLEMENTARY INFORMATION: Detailed tutorials, LDA help system and examples are distributed within LDA software. For Macintosh OS X user, the Jre version 1.4 can be downloaded from http://connect.apple.com.     

hzar: hybrid zone analysis using an R software package

We present a new software package (hzar ) that provides functions for fitting molecular genetic and morphological data from hybrid zones to classic equilibrium cline models using the Metropolis–Hastings Markov chain Monte Carlo (MCMC) algorithm. The software applies likelihood functions appropriate for different types of data, including diploid and haploid genetic markers and quantitative morphological traits. The modular design allows flexibility in fitting cline models of varying complexity. To facilitate hypothesis testing, an autofit function is included that allows automated model selection from a set of nested cline models. Cline parameter values, such as cline centre and cline width, are estimated and may be compared statistically across clines. The package is written in the R language and is available through the Comprehensive R Archive Network (CRAN; http://cran.r-project.org/ ). Here, we describe hzar and demonstrate its use with a sample data set from a well‐studied hybrid zone in western Panama between white‐collared (Manacus candei) and golden‐collared manakins (M. vitellinus). Comparisons of our results with previously published results for this hybrid zone validate the hzar software. We extend analysis of this hybrid zone by fitting additional models to molecular data where appropriate.     

An overview of the utility of population simulation software in molecular ecology

Stochastic simulation software that simultaneously model genetic, population and environmental processes can inform many topics in molecular ecology. These include forecasting species and community response to environmental change, inferring dispersal ecology, revealing cryptic mating, quantifying past population dynamics, assessing in situ management options and monitoring neutral and adaptive biodiversity change. Advances in population demographic–genetic simulation software, especially with respect to individual life history, landscapes and genetic processes, are transforming and expanding the ways that molecular data can be used. The aim of this review is to explain the roles that such software can play in molecular ecology studies (whether as a principal component or a supporting function) so that researchers can decide whether, when and precisely how simulations can be incorporated into their work. First, I use seven case studies to demonstrate how simulations are employed, their specific advantage/necessity and what alternative or complementary (nonsimulation) approaches are available. I also explain how simulations can be integrated with existing spatial, environmental, historical and genetic data sets. I next describe simulation features that may be of interest to molecular ecologists, such as spatial and behavioural considerations and species' interactions, to provide guidance on how particular simulation capabilities can serve particular needs. Lastly, I discuss the prospect of simulation software in emerging challenges (climate change, biodiversity monitoring, population exploitation) and opportunities (genomics, ancient DNA), in order to emphasize that the scope of simulation‐based work is expanding. I also suggest practical considerations, priorities and elements of best practice. This should accelerate the uptake of simulation approaches and firmly embed them as a versatile tool in the molecular ecologist's toolbox.     

CORAL: Building up QSAR models for the chromosome aberration test

A high level of chromosomal aberrations in peripheral blood lymphocytes may be an early marker of cancer risk, but data on risk of specific cancers and types of chromosomal aberrations are limited. Consequently, the development of predictive models for chromosomal aberrations test is important task. Majority of models for chromosomal aberrations test are so-called knowledge-based rules system. The CORAL software (http://www.insilico.eu/coral, abbreviation of “CORrelation And Logic”) is an alternative for knowledge-based rules system. In contrast to knowledge-based rules system, the CORAL software gives possibility to estimate the influence upon the predictive potential of a model of different molecular alerts as well as different splits into the training set and validation set. This possibility is not available for the approaches based on the knowledge-based rules system. Quantitative Structure–Activity Relationships (QSAR) for chromosome aberration test are established for five random splits into the training, calibration, and validation sets. The QSAR approach is based on representation of the molecular structure by simplified molecular input-line entry system (SMILES) without data on physicochemical and/or biochemical parameters. In spite of this limitation, the statistical quality of these models is quite good.     

swinger: a user‐friendly computer program to establish captive breeding groups that minimize relatedness without pedigree information

Captive breeding programmes are often a necessity for the continued persistence of a population or species. They typically have the goal of maintaining genetic diversity and minimizing inbreeding. However, most captive breeding programmes have been based on the assumption that the founding breeders are unrelated and outbred, even though in situ anthropogenic impacts often mean these founders may have high relatedness and substantial inbreeding. In addition, polygamous group‐breeding species in captivity often have uncertain pedigrees, making it difficult to select the group composition for subsequent breeding. Molecular‐based estimates of relatedness and inbreeding may instead be used to select breeding groups (≥two individuals) that minimize relatedness and filter out inbred individuals. swinger constructs breeding groups based on molecular estimates of relatedness and inbreeding. The number of possible combinations of breeding groups quickly becomes intractable by hand. swinger was designed to overcome this major issue in ex situ conservation biology. The user can specify parameters within swinger to reach breeding solutions that suit the mating system of the target species and available resources. We provide evidence of the efficiency of the software with an empirical example and using simulations. The only data required are a typical molecular marker data set, such as a microsatellite or SNP data set, from which estimates of inbreeding and pairwise relatedness may be obtained. Such molecular data sets are becoming easier to gather from non‐model organisms with next‐generation sequencing technology. swinger is an open‐source software with a user‐friendly interface and is available at http://www.molecularecology.flinders.edu.au/molecular-ecology-lab/software/swinger/swinger/ and https://github.com/Yuma248/Swinger .     

StAMPP: an R package for calculation of genetic differentiation and structure of mixed‐ploidy level populations

Statistical Analysis of Mixed‐Ploidy Populations (StAMPP) is a freely available R package for calculation of population structure and differentiation based on single nucleotide polymorphism (SNP) genotype data from populations of any ploidy level, and/or mixed‐ploidy levels. StAMPP provides an advance on previous similar software packages, due to an ability to calculate pairwise F_ST values along with confidence intervals, Nei's genetic distance and genomic relationship matrixes from data sets of mixed‐ploidy level. The software code is designed to efficiently handle analysis of large genotypic data sets that are typically generated by high‐throughput genotyping platforms. Population differentiation studies using StAMPP are broadly applicable to studies of molecular ecology and conservation genetics, as well as animal and plant breeding.     

Alignment of molecular networks by integer quadratic programming

MOTIVATION: With more and more data on molecular networks (e.g. protein interaction networks, gene regulatory networks and metabolic networks) available, the discovery of conserved patterns or signaling pathways by comparing various kinds of networks among different species or within a species becomes an increasingly important problem. However, most of the conventional approaches either restrict comparative analysis to special structures, such as pathways, or adopt heuristic algorithms due to computational burden. RESULTS: In this article, to find the conserved substructures, we develop an efficient algorithm for aligning molecular networks based on both molecule similarity and architecture similarity, by using integer quadratic programming (IQP). Such an IQP can be relaxed into the corresponding quadratic programming (QP) which almost always ensures an integer solution, thereby making molecular network alignment tractable without any approximation. The proposed framework is very flexible and can be applied to many kinds of molecular networks including weighted and unweighted, directed and undirected networks with or without loops. AVAILABILITY: Matlab code and data are available from http://zhangroup.aporc.org/bioinfo/MNAligner or http://intelligent.eic.osaka-sandai.ac.jp/chenen/software/MNAligner, or upon request from authors. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.