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1.  Constructing perfect phylogenies and proper triangulations for three-state characters 
In this paper, we study the problem of constructing perfect phylogenies for three-state characters. Our work builds on two recent results. The first result states that for three-state characters, the local condition of examining all subsets of three characters is sufficient to determine the global property of admitting a perfect phylogeny. The second result applies tools from minimal triangulation theory to the partition intersection graph to determine if a perfect phylogeny exists. Despite the wealth of combinatorial tools and algorithms stemming from the chordal graph and minimal triangulation literature, it is unclear how to use such approaches to efficiently construct a perfect phylogeny for three-state characters when the data admits one. We utilize structural properties of both the partition intersection graph and the original data in order to achieve a competitive time bound.
doi:10.1186/1748-7188-7-26
PMCID: PMC3558378  PMID: 23006612
Perfect phylogeny; Chordal graph; Minimal triangulation; Minimal separator
2.  Haplotype reconstruction using perfect phylogeny and sequence data 
BMC Bioinformatics  2012;13(Suppl 6):S3.
Haplotype phasing is a well studied problem in the context of genotype data. With the recent developments in high-throughput sequencing, new algorithms are needed for haplotype phasing, when the number of samples sequenced is low and when the sequencing coverage is blow. High-throughput sequencing technologies enables new possibilities for the inference of haplotypes. Since each read is originated from a single chromosome, all the variant sites it covers must derive from the same haplotype. Moreover, the sequencing process yields much higher SNP density than previous methods, resulting in a higher correlation between neighboring SNPs. We offer a new approach for haplotype phasing, which leverages on these two properties. Our suggested algorithm, called Perfect Phlogeny Haplotypes from Sequencing (PPHS) uses a perfect phylogeny model and it models the sequencing errors explicitly. We evaluated our method on real and simulated data, and we demonstrate that the algorithm outperforms previous methods when the sequencing error rate is high or when coverage is low.
doi:10.1186/1471-2105-13-S6-S3
PMCID: PMC3330028  PMID: 22537042
3.  Minimum Contradiction Matrices in Whole Genome Phylogenies 
Minimum contradiction matrices are a useful complement to distance-based phylogenies. A minimum contradiction matrix represents phylogenetic information under the form of an ordered distance matrix Yi, jn. A matrix element corresponds to the distance from a reference vertex n to the path (i, j). For an X-tree or a split network, the minimum contradiction matrix is a Robinson matrix. It therefore fulfills all the inequalities defining perfect order: Yi, jn ≥ Yi,kn, Yk jn ≥ Yk, In, i ≤ j ≤ k < n. In real phylogenetic data, some taxa may contradict the inequalities for perfect order. Contradictions to perfect order correspond to deviations from a tree or from a split network topology. Efficient algorithms that search for the best order are presented and tested on whole genome phylogenies with 184 taxa including many Bacteria, Archaea and Eukaryota. After optimization, taxa are classified in their correct domain and phyla. Several significant deviations from perfect order correspond to well-documented evolutionary events.
PMCID: PMC2614196  PMID: 19204821
phylogenetic trees; whole genome phylogeny; minimum contradiction; split network
4.  Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots 
Background
Although taxonomy is often used informally to evaluate the results of phylogenetic inference and the root of phylogenetic trees, algorithmic methods to do so are lacking.
Results
In this paper we formalize these procedures and develop algorithms to solve the relevant problems. In particular, we introduce a new algorithm that solves a "subcoloring" problem to express the difference between a taxonomy and a phylogeny at a given rank. This algorithm improves upon the current best algorithm in terms of asymptotic complexity for the parameter regime of interest; we also describe a branch-and-bound algorithm that saves orders of magnitude in computation on real data sets. We also develop a formalism and an algorithm for rooting phylogenetic trees according to a taxonomy.
Conclusions
The algorithms in this paper, and the associated freely-available software, will help biologists better use and understand taxonomically labeled phylogenetic trees.
doi:10.1186/1748-7188-7-8
PMCID: PMC3384453  PMID: 22549005
phylogenetics; taxononomy; dynamic program; branch and bound; convex coloring; algorithms
5.  FRANz: reconstruction of wild multi-generation pedigrees 
Bioinformatics  2009;25(16):2134-2139.
Summary: We present a software package for pedigree reconstruction in natural populations using co-dominant genomic markers such as microsatellites and single nucleotide polymorphisms (SNPs). If available, the algorithm makes use of prior information such as known relationships (sub-pedigrees) or the age and sex of individuals. Statistical confidence is estimated by Markov Chain Monte Carlo (MCMC) sampling. The accuracy of the algorithm is demonstrated for simulated data as well as an empirical dataset with known pedigree. The parentage inference is robust even in the presence of genotyping errors.
Availability: The C source code of FRANz can be obtained under the GPL from http://www.bioinf.uni-leipzig.de/Software/FRANz/.
Contact: markus@bioinf.uni-leipzig.de
doi:10.1093/bioinformatics/btp064
PMCID: PMC2722992  PMID: 19202194
6.  A double classification tree search algorithm for index SNP selection 
BMC Bioinformatics  2004;5:89.
Background
In population-based studies, it is generally recognized that single nucleotide polymorphism (SNP) markers are not independent. Rather, they are carried by haplotypes, groups of SNPs that tend to be coinherited. It is thus possible to choose a much smaller number of SNPs to use as indices for identifying haplotypes or haplotype blocks in genetic association studies. We refer to these characteristic SNPs as index SNPs. In order to reduce costs and work, a minimum number of index SNPs that can distinguish all SNP and haplotype patterns should be chosen. Unfortunately, this is an NP-complete problem, requiring brute force algorithms that are not feasible for large data sets.
Results
We have developed a double classification tree search algorithm to generate index SNPs that can distinguish all SNP and haplotype patterns. This algorithm runs very rapidly and generates very good, though not necessarily minimum, sets of index SNPs, as is to be expected for such NP-complete problems.
Conclusions
A new algorithm for index SNP selection has been developed. A webserver for index SNP selection is available at
doi:10.1186/1471-2105-5-89
PMCID: PMC476734  PMID: 15238162
7.  HapScope: a software system for automated and visual analysis of functionally annotated haplotypes 
Nucleic Acids Research  2002;30(23):5213-5221.
We have developed a software analysis package, HapScope, which includes a comprehensive analysis pipeline and a sophisticated visualization tool for analyzing functionally annotated haplotypes. The HapScope analysis pipeline supports: (i) computational haplotype construction with an expectation-maximization or Bayesian statistical algorithm; (ii) SNP classification by protein coding change, homology to model organisms or putative regulatory regions; and (iii) minimum SNP subset selection by either a Brute Force Algorithm or a Greedy Partition Algorithm. The HapScope viewer displays genomic structure with haplotype information in an integrated environment, providing eight alternative views for assessing genetic and functional correlation. It has a user-friendly interface for: (i) haplotype block visualization; (ii) SNP subset selection; (iii) haplotype consolidation with subset SNP markers; (iv) incorporation of both experimentally determined haplotypes and computational results; and (v) data export for additional analysis. Comparison of haplotypes constructed by the statistical algorithms with those determined experimentally shows variation in haplotype prediction accuracies in genomic regions with different levels of nucleotide diversity. We have applied HapScope in analyzing haplotypes for candidate genes and genomic regions with extensive SNP and genotype data. We envision that the systematic approach of integrating functional genomic analysis with population haplotypes, supported by HapScope, will greatly facilitate current genetic disease research.
PMCID: PMC137968  PMID: 12466546
8.  Parallel Clustering Algorithm for Large-Scale Biological Data Sets 
PLoS ONE  2014;9(4):e91315.
Backgrounds
Recent explosion of biological data brings a great challenge for the traditional clustering algorithms. With increasing scale of data sets, much larger memory and longer runtime are required for the cluster identification problems. The affinity propagation algorithm outperforms many other classical clustering algorithms and is widely applied into the biological researches. However, the time and space complexity become a great bottleneck when handling the large-scale data sets. Moreover, the similarity matrix, whose constructing procedure takes long runtime, is required before running the affinity propagation algorithm, since the algorithm clusters data sets based on the similarities between data pairs.
Methods
Two types of parallel architectures are proposed in this paper to accelerate the similarity matrix constructing procedure and the affinity propagation algorithm. The memory-shared architecture is used to construct the similarity matrix, and the distributed system is taken for the affinity propagation algorithm, because of its large memory size and great computing capacity. An appropriate way of data partition and reduction is designed in our method, in order to minimize the global communication cost among processes.
Result
A speedup of 100 is gained with 128 cores. The runtime is reduced from serval hours to a few seconds, which indicates that parallel algorithm is capable of handling large-scale data sets effectively. The parallel affinity propagation also achieves a good performance when clustering large-scale gene data (microarray) and detecting families in large protein superfamilies.
doi:10.1371/journal.pone.0091315
PMCID: PMC3976248  PMID: 24705246
9.  Direct maximum parsimony phylogeny reconstruction from genotype data 
BMC Bioinformatics  2007;8:472.
Background
Maximum parsimony phylogenetic tree reconstruction from genetic variation data is a fundamental problem in computational genetics with many practical applications in population genetics, whole genome analysis, and the search for genetic predictors of disease. Efficient methods are available for reconstruction of maximum parsimony trees from haplotype data, but such data are difficult to determine directly for autosomal DNA. Data more commonly is available in the form of genotypes, which consist of conflated combinations of pairs of haplotypes from homologous chromosomes. Currently, there are no general algorithms for the direct reconstruction of maximum parsimony phylogenies from genotype data. Hence phylogenetic applications for autosomal data must therefore rely on other methods for first computationally inferring haplotypes from genotypes.
Results
In this work, we develop the first practical method for computing maximum parsimony phylogenies directly from genotype data. We show that the standard practice of first inferring haplotypes from genotypes and then reconstructing a phylogeny on the haplotypes often substantially overestimates phylogeny size. As an immediate application, our method can be used to determine the minimum number of mutations required to explain a given set of observed genotypes.
Conclusion
Phylogeny reconstruction directly from unphased data is computationally feasible for moderate-sized problem instances and can lead to substantially more accurate tree size inferences than the standard practice of treating phasing and phylogeny construction as two separate analysis stages. The difference between the approaches is particularly important for downstream applications that require a lower-bound on the number of mutations that the genetic region has undergone.
doi:10.1186/1471-2105-8-472
PMCID: PMC2222657  PMID: 18053244
10.  Comparative modelling by restraint-based conformational sampling 
Background
Although comparative modelling is routinely used to produce three-dimensional models of proteins, very few automated approaches are formulated in a way that allows inclusion of restraints derived from experimental data as well as those from the structures of homologues. Furthermore, proteins are usually described as a single conformer, rather than an ensemble that represents the heterogeneity and inaccuracy of experimentally determined protein structures. Here we address these issues by exploring the application of the restraint-based conformational space search engine, RAPPER, which has previously been developed for rebuilding experimentally defined protein structures and for fitting models to electron density derived from X-ray diffraction analyses.
Results
A new application of RAPPER for comparative modelling uses positional restraints and knowledge-based sampling to generate models with accuracies comparable to other leading modelling tools. Knowledge-based predictions are based on geometrical features of the homologous templates and rules concerning main-chain and side-chain conformations. By directly changing the restraints derived from available templates we estimate the accuracy limits of the method in comparative modelling.
Conclusion
The application of RAPPER to comparative modelling provides an effective means of exploring the conformational space available to a target sequence. Enhanced methods for generating positional restraints can greatly improve structure prediction. Generation of an ensemble of solutions that are consistent with both target sequence and knowledge derived from the template structures provides a more appropriate representation of a structural prediction than a single model. By formulating homologous structural information as sets of restraints we can begin to consider how comparative models might be used to inform conformer generation from sparse experimental data.
doi:10.1186/1472-6807-8-7
PMCID: PMC2275734  PMID: 18237407
11.  SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data 
BMC Genomics  2014;15:162.
Background
Phylogenetic trees are widely used for genetic and evolutionary studies in various organisms. Advanced sequencing technology has dramatically enriched data available for constructing phylogenetic trees based on single nucleotide polymorphisms (SNPs). However, massive SNP data makes it difficult to perform reliable analysis, and there has been no ready-to-use pipeline to generate phylogenetic trees from these data.
Results
We developed a new pipeline, SNPhylo, to construct phylogenetic trees based on large SNP datasets. The pipeline may enable users to construct a phylogenetic tree from three representative SNP data file formats. In addition, in order to increase reliability of a tree, the pipeline has steps such as removing low quality data and considering linkage disequilibrium. A maximum likelihood method for the inference of phylogeny is also adopted in generation of a tree in our pipeline.
Conclusions
Using SNPhylo, users can easily produce a reliable phylogenetic tree from a large SNP data file. Thus, this pipeline can help a researcher focus more on interpretation of the results of analysis of voluminous data sets, rather than manipulations necessary to accomplish the analysis.
doi:10.1186/1471-2164-15-162
PMCID: PMC3945939  PMID: 24571581
Polymorphisms; Linkage disequilibrium; Maximum likelihood
12.  MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics 
BMC Bioinformatics  2010;11:379.
Background
The development, in the last decade, of stochastic heuristics implemented in robust application softwares has made large phylogeny inference a key step in most comparative studies involving molecular sequences. Still, the choice of a phylogeny inference software is often dictated by a combination of parameters not related to the raw performance of the implemented algorithm(s) but rather by practical issues such as ergonomics and/or the availability of specific functionalities.
Results
Here, we present MetaPIGA v2.0, a robust implementation of several stochastic heuristics for large phylogeny inference (under maximum likelihood), including a Simulated Annealing algorithm, a classical Genetic Algorithm, and the Metapopulation Genetic Algorithm (metaGA) together with complex substitution models, discrete Gamma rate heterogeneity, and the possibility to partition data. MetaPIGA v2.0 also implements the Likelihood Ratio Test, the Akaike Information Criterion, and the Bayesian Information Criterion for automated selection of substitution models that best fit the data. Heuristics and substitution models are highly customizable through manual batch files and command line processing. However, MetaPIGA v2.0 also offers an extensive graphical user interface for parameters setting, generating and running batch files, following run progress, and manipulating result trees. MetaPIGA v2.0 uses standard formats for data sets and trees, is platform independent, runs in 32 and 64-bits systems, and takes advantage of multiprocessor and multicore computers.
Conclusions
The metaGA resolves the major problem inherent to classical Genetic Algorithms by maintaining high inter-population variation even under strong intra-population selection. Implementation of the metaGA together with additional stochastic heuristics into a single software will allow rigorous optimization of each heuristic as well as a meaningful comparison of performances among these algorithms. MetaPIGA v2.0 gives access both to high customization for the phylogeneticist, as well as to an ergonomic interface and functionalities assisting the non-specialist for sound inference of large phylogenetic trees using nucleotide sequences. MetaPIGA v2.0 and its extensive user-manual are freely available to academics at http://www.metapiga.org.
doi:10.1186/1471-2105-11-379
PMCID: PMC2912891  PMID: 20633263
13.  Minimizing Contradictions on Circular Order of Phylogenic Trees 
Distance-based approaches to phylogeny use estimations of the evolutionary distance between sequences to reconstruct an evolution tree. If the evolution can be represented by an X-tree, the different sequences can be ordered so that the distance matrix Yi, jn, representing the distance from a leaf n to the path (i, j), is perfectly ordered meaning that Yi, jn ≥ Yi, kn and Yk, jn ≥ Yk, in for i ≤ j ≤ k. After ordering of the sequences, the distance matrix Yi, jn permits to visualize phylogenetic relationships between taxa and to localize deviations from perfect order. The effect of perturbations resulting from lateral gene transfer or crossover can be modeled probabilistically. The order is shown to be quite robust against many perturbations. We have developed algorithms to minimize the level of contradiction in the order of the sequences. These algorithms are tested on the SSU rRNA data for Archaea. The degree of contradiction after optimization is for most taxa quite low. Regions in the taxa space with deviations from perfect order were identified.
PMCID: PMC2684138  PMID: 19468311
phylogenetics; circular order; distance-based estimation; lateral gene transfer
14.  PGA: power calculator for case-control genetic association analyses 
BMC Genetics  2008;9:36.
Background
Statistical power calculations inform the design and interpretation of genetic association studies, but few programs are tailored to case-control studies of single nucleotide polymorphisms (SNPs) in unrelated subjects.
Results
We have developed the "Power for Genetic Association analyses" (PGA) package which comprises algorithms and graphical user interfaces for sample size and minimum detectable risk calculations using SNP or haplotype effects under different genetic models and study constrains. The software accounts for linkage disequilibrium and statistical multiple comparisons. The results are presented in graphs or tables and can be printed or exported in standard file formats.
Conclusion
PGA is user friendly software that can facilitate decision making for association studies of candidate genes, fine-mapping studies, and whole-genome scans. Stand-alone executable files and a Matlab toolbox are available for download at:
doi:10.1186/1471-2156-9-36
PMCID: PMC2387159  PMID: 18477402
15.  MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features 
Nucleic Acids Research  2007;35(Web Server issue):W339-W344.
To distinguish the real pre-miRNAs from other hairpin sequences with similar stem-loops (pseudo pre-miRNAs), a hybrid feature which consists of local contiguous structure-sequence composition, minimum of free energy (MFE) of the secondary structure and P-value of randomization test is used. Besides, a novel machine-learning algorithm, random forest (RF), is introduced. The results suggest that our method predicts at 98.21% specificity and 95.09% sensitivity. When compared with the previous study, Triplet-SVM-classifier, our RF method was nearly 10% greater in total accuracy. Further analysis indicated that the improvement was due to both the combined features and the RF algorithm. The MiPred web server is available at http://www.bioinf.seu.edu.cn/miRNA/. Given a sequence, MiPred decides whether it is a pre-miRNA-like hairpin sequence or not. If the sequence is a pre-miRNA-like hairpin, the RF classifier will predict whether it is a real pre-miRNA or a pseudo one.
doi:10.1093/nar/gkm368
PMCID: PMC1933124  PMID: 17553836
16.  Rec-DCM-Eigen: Reconstructing a Less Parsimonious but More Accurate Tree in Shorter Time 
PLoS ONE  2011;6(8):e22483.
Maximum parsimony (MP) methods aim to reconstruct the phylogeny of extant species by finding the most parsimonious evolutionary scenario using the species' genome data. MP methods are considered to be accurate, but they are also computationally expensive especially for a large number of species. Several disk-covering methods (DCMs), which decompose the input species to multiple overlapping subgroups (or disks), have been proposed to solve the problem in a divide-and-conquer way.
We design a new DCM based on the spectral method and also develop the COGNAC (Comparing Orders of Genes using Novel Algorithms and high-performance Computers) software package. COGNAC uses the new DCM to reduce the phylogenetic tree search space and selects an output tree from the reduced search space based on the MP principle. We test the new DCM using gene order data and inversion distance. The new DCM not only reduces the number of candidate tree topologies but also excludes erroneous tree topologies which can be selected by original MP methods. Initial labeling of internal genomes affects the accuracy of MP methods using gene order data, and the new DCM enables more accurate initial labeling as well. COGNAC demonstrates superior accuracy as a consequence. We compare COGNAC with FastME and the combination of the state of the art DCM (Rec-I-DCM3) and GRAPPA . COGNAC clearly outperforms FastME in accuracy. COGNAC –using the new DCM–also reconstructs a much more accurate tree in significantly shorter time than GRAPPA with Rec-I-DCM3.
doi:10.1371/journal.pone.0022483
PMCID: PMC3160844  PMID: 21887219
17.  HTreeQA: Using Semi-Perfect Phylogeny Trees in Quantitative Trait Loci Study on Genotype Data 
G3: Genes|Genomes|Genetics  2012;2(2):175-189.
With the advances in high-throughput genotyping technology, the study of quantitative trait loci (QTL) has emerged as a promising tool to understand the genetic basis of complex traits. Methodology development for the study of QTL recently has attracted significant research attention. Local phylogeny-based methods have been demonstrated to be powerful tools for uncovering significant associations between phenotypes and single-nucleotide polymorphism markers. However, most existing methods are designed for homozygous genotypes, and a separate haplotype reconstruction step is often needed to resolve heterozygous genotypes. This approach has limited power to detect nonadditive genetic effects and imposes an extensive computational burden. In this article, we propose a new method, HTreeQA, that uses a tristate semi-perfect phylogeny tree to approximate the perfect phylogeny used in existing methods. The semi-perfect phylogeny trees are used as high-level markers for association study. HTreeQA uses the genotype data as direct input without phasing. HTreeQA can handle complex local population structures. It is suitable for QTL mapping on any mouse populations, including the incipient Collaborative Cross lines. Applied HTreeQA, significant QTLs are found for two phenotypes of the PreCC lines, white head spot and running distance at day 5/6. These findings are consistent with known genes and QTL discovered in independent studies. Simulation studies under three different genetic models show that HTreeQA can detect a wider range of genetic effects and is more efficient than existing phylogeny-based approaches. We also provide rigorous theoretical analysis to show that HTreeQA has a lower error rate than alternative methods.
doi:10.1534/g3.111.001768
PMCID: PMC3284325  PMID: 22384396
phylogeny; quantitative trait loci (QTL); Mouse Collaborative Cross; Mouse Genetic Resource
18.  MixtureTree: a program for constructing phylogeny 
BMC Bioinformatics  2011;12:111.
Background
MixtureTree v1.0 is a Linux based program (written in C++) which implements an algorithm based on mixture models for reconstructing phylogeny from binary sequence data, such as single-nucleotide polymorphisms (SNPs). In addition to the mixture algorithm with three different optimization options, the program also implements a bootstrap procedure with majority-rule consensus.
Results
The MixtureTree program written in C++ is a Linux based package. The User's Guide and source codes will be available at http://math.asu.edu/~scchen/MixtureTree.html
Conclusions
The efficiency of the mixture algorithm is relatively higher than some classical methods, such as Neighbor-Joining method, Maximum Parsimony method and Maximum Likelihood method. The shortcoming of the mixture tree algorithms, for example timing consuming, can be improved by implementing other revised Expectation-Maximization(EM) algorithms instead of the traditional EM algorithm.
doi:10.1186/1471-2105-12-111
PMCID: PMC3102041  PMID: 21615972
19.  WinHAP: An Efficient Haplotype Phasing Algorithm Based on Scalable Sliding Windows 
PLoS ONE  2012;7(8):e43163.
Haplotype phasing represents an essential step in studying the association of genomic polymorphisms with complex genetic diseases, and in determining targets for drug designing. In recent years, huge amounts of genotype data are produced from the rapidly evolving high-throughput sequencing technologies, and the data volume challenges the community with more efficient haplotype phasing algorithms, in the senses of both running time and overall accuracy. 2SNP is one of the fastest haplotype phasing algorithms with comparable low error rates with the other algorithms. The most time-consuming step of 2SNP is the construction of a maximum spanning tree (MST) among all the heterozygous SNP pairs. We simplified this step by replacing the MST with the initial haplotypes of adjacent heterozygous SNP pairs. The multi-SNP haplotypes were estimated within a sliding window along the chromosomes. The comparative studies on four different-scale genotype datasets suggest that our algorithm WinHAP outperforms 2SNP and most of the other haplotype phasing algorithms in terms of both running speeds and overall accuracies. To facilitate the WinHAP’s application in more practical biological datasets, we released the software for free at: http://staff.ustc.edu.cn/~xuyun/winhap/index.htm.
doi:10.1371/journal.pone.0043163
PMCID: PMC3419172  PMID: 22905221
20.  A hierarchical model for incomplete alignments in phylogenetic inference 
Bioinformatics  2009;25(5):592-598.
Motivation: Full-length DNA and protein sequences that span the entire length of a gene are ideally used for multiple sequence alignments (MSAs) and the subsequent inference of their relationships. Frequently, however, MSAs contain a substantial amount of missing data. For example, expressed sequence tags (ESTs), which are partial sequences of expressed genes, are the predominant source of sequence data for many organisms. The patterns of missing data typical for EST-derived alignments greatly compromise the accuracy of estimated phylogenies.
Results: We present a statistical method for inferring phylogenetic trees from EST-based incomplete MSA data. We propose a class of hierarchical models for modeling pairwise distances between the sequences, and develop a fully Bayesian approach for estimation of the model parameters. Once the distance matrix is estimated, the phylogenetic tree may be constructed by applying neighbor-joining (or any other algorithm of choice). We also show that maximizing the marginal likelihood from the Bayesian approach yields similar results to a profile likelihood estimation. The proposed methods are illustrated using simulated protein families, for which the true phylogeny is known, and one real protein family.
Availability: R code for fitting these models are available from: http://people.bu.edu/gupta/software.htm.
Contact: gupta@bu.edu
Supplementary information: Supplemantary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btp015
PMCID: PMC2647833  PMID: 19147663
21.  snp-search: simple processing, manipulation and searching of SNPs from high-throughput sequencing 
BMC Bioinformatics  2013;14:326.
Background
A typical bacterial pathogen genome mapping project can identify thousands of single nucleotide polymorphisms (SNP). Interpreting SNP data is complex and it is difficult to conceptualise the data contained within the large flat files that are the typical output from most SNP calling algorithms. One solution to this problem is to construct a database that can be queried using simple commands so that SNP interrogation and output is both easy and comprehensible.
Results
Here we present snp-search, a tool that manages SNP data and allows for manipulation and searching of SNP data. After creation of a SNP database from a VCF file, snp-search can be used to convert the selected SNP data into FASTA sequences, construct phylogenies, look for unique SNPs, and output contextual information about each SNP. The FASTA output from snp-search is particularly useful for the generation of robust phylogenetic trees that are based on SNP differences across the conserved positions in whole genomes. Queries can be designed to answer critical genomic questions such as the association of SNPs with particular phenotypes.
Conclusions
snp-search is a tool that manages SNP data and outputs useful information which can be used to test important biological hypotheses.
doi:10.1186/1471-2105-14-326
PMCID: PMC3840589  PMID: 24246037
Single Nucleotide Polymorphisms (SNP); Variant Call Format (VCF); SQL database; High-throughput Sequencing; Next Generation Sequencing (NGS); Ruby; Phylogeny
22.  TREEQA: QUANTITATIVE GENOME WIDE ASSOCIATION MAPPING USING LOCAL PERFECT PHYLOGENY TREES 
The goal of genome wide association (GWA) mapping in modern genetics is to identify genes or narrow regions in the genome that contribute to genetically complex phenotypes such as morphology or disease. Among the existing methods, tree-based association mapping methods show obvious advantages over single marker-based and haplotype-based methods because they incorporate information about the evolutionary history of the genome into the analysis. However, existing tree-based methods are designed primarily for binary phenotypes derived from case/control studies or fail to scale genome-wide.
In this paper, we introduce TreeQA, a quantitative GWA mapping algorithm. TreeQA utilizes local perfect phylogenies constructed in genomic regions exhibiting no evidence of historical recombination. By efficient algorithm design and implementation, TreeQA can efficiently conduct quantitative genom-wide association analysis and is more effective than the previous methods. We conducted extensive experiments on both simulated datasets and mouse inbred lines to demonstrate the efficiency and effectiveness of TreeQA.
PMCID: PMC2739990  PMID: 19209719
23.  An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies 
Background
Recent progress in sequencing and 3 D structure determination techniques stimulated development of approaches aimed at more precise annotation of proteins, that is, prediction of exact specificity to a ligand or, more broadly, to a binding partner of any kind.
Results
We present a method, SDPclust, for identification of protein functional subfamilies coupled with prediction of specificity-determining positions (SDPs). SDPclust predicts specificity in a phylogeny-independent stochastic manner, which allows for the correct identification of the specificity for proteins that are separated on a phylogenetic tree, but still bind the same ligand. SDPclust is implemented as a Web-server http://bioinf.fbb.msu.ru/SDPfoxWeb/ and a stand-alone Java application available from the website.
Conclusions
SDPclust performs a simultaneous identification of specificity determinants and specificity groups in a statistically robust and phylogeny-independent manner.
doi:10.1186/1748-7188-5-29
PMCID: PMC2914642  PMID: 20633297
24.  htSNPer1.0: software for haplotype block partition and htSNPs selection 
BMC Bioinformatics  2005;6:38.
Background
There is recently great interest in haplotype block structure and haplotype tagging SNPs (htSNPs) in the human genome for its implication on htSNPs-based association mapping strategy for complex disease. Different definitions have been used to characterize the haplotype block structure in the human genome, and several different performance criteria and algorithms have been suggested on htSNPs selection.
Results
A heuristic algorithm, generalized branch-and-bound algorithm, is applied to the searching of minimal set of haplotype tagging SNPs (htSNPs) according to different htSNPs performance criteria. We develop a software htSNPer1.0 to implement the algorithm, and integrate three htSNPs performance criteria and four haplotype block definitions for haplotype block partitioning. It is a software with powerful Graphical User Interface (GUI), which can be used to characterize the haplotype block structure and select htSNPs in the candidate gene or interested genomic regions. It can find the global optimization with only a fraction of the computing time consumed by exhaustive searching algorithm.
Conclusion
htSNPer1.0 allows molecular geneticists to perform haplotype block analysis and htSNPs selection using different definitions and performance criteria. The software is a powerful tool for those focusing on association mapping based on strategy of haplotype block and htSNPs.
doi:10.1186/1471-2105-6-38
PMCID: PMC1274247  PMID: 15740612
25.  Fast computation of distance estimators 
BMC Bioinformatics  2007;8:89.
Background
Some distance methods are among the most commonly used methods for reconstructing phylogenetic trees from sequence data. The input to a distance method is a distance matrix, containing estimated pairwise distances between all pairs of taxa. Distance methods themselves are often fast, e.g., the famous and popular Neighbor Joining (NJ) algorithm reconstructs a phylogeny of n taxa in time O(n3). Unfortunately, the fastest practical algorithms known for Computing the distance matrix, from n sequences of length l, takes time proportional to l·n2. Since the sequence length typically is much larger than the number of taxa, the distance estimation is the bottleneck in phylogeny reconstruction. This bottleneck is especially apparent in reconstruction of large phylogenies or in applications where many trees have to be reconstructed, e.g., bootstrapping and genome wide applications.
Results
We give an advanced algorithm for Computing the number of mutational events between DNA sequences which is significantly faster than both Phylip and Paup. Moreover, we give a new method for estimating pairwise distances between sequences which contain ambiguity Symbols. This new method is shown to be more accurate as well as faster than earlier methods.
Conclusion
Our novel algorithm for Computing distance estimators provides a valuable tool in phylogeny reconstruction. Since the running time of our distance estimation algorithm is comparable to that of most distance methods, the previous bottleneck is removed. All distance methods, such as NJ, require a distance matrix as input and, hence, our novel algorithm significantly improves the overall running time of all distance methods. In particular, we show for real world biological applications how the running time of phylogeny reconstruction using NJ is improved from a matter of hours to a matter of seconds.
doi:10.1186/1471-2105-8-89
PMCID: PMC1831791  PMID: 17355623

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