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Showing results for: [ Bioinformatics Software ]
This collection includes data to support the paper on the Kelpie software which reconstructs amplicons from metagenomes. Specifically, the collection includes three zip files which includes pair-mer... moreged amplicon data for the 3 samples; the corresponding 16S-filtered WGS data and the original metagenomes. The three formation water samples in the data labelled as: W1, W2, W3 – and their respective basins/CSMB refs are in the Kelpie manuscript.less
Legacy data - Bacterial genomics - Published 26 Jun 2018
A program for analysing compositional heterogeneity across aligned sequence data. Most model-based molecular phylogenetic methods assume evolution under stationary, reversible, and globally homogeneo... moreus conditions, implying that it would be unwise to use these methods if the data evolved under more complex conditions. Homo allows users to test whether pairs of sequences in alignments of nucleotides or amino acids are consistent with evolution under stationary, reversible, and globally homogeneous conditions (for details, see Ababneh et al. 2006b). The output is a: Brief summary (printed to the terminal); Full summary (printed to a file); Five tables (printed to files), one with the p-values and four with the compositional distances. The summaries allow users to determine whether some of the sequences violate the assumption of evolution under stationary, reversible, and globally homogeneous conditions. For further details, see the manual, which is included with the software.less
CLSD Strategic: Solving Biodiversity Cha - Bioinformatics Software - Published 11 Jan 2018
AliStat has been written to allow users to evaluate how complete their multiple sequence alignments (MSA) of nucleotides or amino acids are. In particular, AliStat allows a user to generate four usef... moreul metrics (i.e. the completeness of an MSA (Ca), of a row in an MSA (Cr), of a column in an MSA (Cc), and of homologous sites in a sub-alignment of sequences i and j (Cij)), each of which will tell the user something useful about the distribution of missing data in an MSA. The information thus obtained can be used to make educated decisions about how the data in the MSA should be analysed phylogenetically. The output is a set of informative figures, tables, and sub-alignments. In addition, AliStat produces information that meets the Minimum Reporting Standard (MRS) for MSAs, a concept that we introduce in Wong TFK, Kalyaanamoorthy S, Meusemann K, Yeates DK, Misof B, Jermiin LS. 2017. AliStat: Quality-control metrics for multiple sequence alignments. Nature Methods (in prep).less
CLSD Strategic: Solving Biodiversity Cha - Bioinformatics Software - Published 02 Jun 2017
HAL-HAS is a program package, comprising HAL-BU, HAL-TD, and HAS, that was written to allow users to infer an optimal model of evolution for a given data set, a given tree. We introduce a family of n... moreon-stationary and non-homogeneous mixture models that approximate the rate Heterogeneity Across Lineages (HAL) and the rate Heterogeneity Across Sites (HAS) without the assumption of an underlying predefined statistical distribution.less
A program to simulate the evolution of DNA under the mixture models of heterogeneity across lineage and heterogeneity across sites. Hetero was written to facilitate the development and testing of phy... morelogenetic methods. In particular, Hetero 2 allows the user to generate nucleotide sequences on a phylogenetic tree under complex conditions. The complexity of the conditions are such that the evolutionary process can differ from site to site in the DNA as well as from edge to edge in the phylogenetic tree, with the evolutionary process being the variable. The output is a set of alignments of nucleotides. For further details, see the manual, which is included with the software.less
A set of machine readable resources that are part of the output of a project undertaken for the Commonwealth Department of Environment, under the Essential Environmental Measures program. These repres... moreent an information model for vegetation sites data, comprising - a UML model in a .EAP file (database for use with Sparx Systems Enterprise Architect) - an OWL Ontology implementation - RDF files (TTL format) of some example data - XML files of the same example dataless
LWF-Water Resource Management-Consultanc - Information model for vegetation sites data - Published 28 Jul 2016
FGS3 (Fast Group-wise Semantic Similarity Search) computes semantic similarity between pairs of genes based on Gene Ontology (GO) annotations. FGS3 use a group-wise similarity measure. It takes two se... morets of annotated genes as input together with a definition of the GO term hierarchy. FGS3 can use one of four different term specificity measures (two corpus-based measures and two structure-based measures). To enable fast similarity search in large sets of genes, FGS3 allows pruning of the search space based on similarity thresholds.less
Aquaculture Molecular Informatics - Transcriptome Analytics - Published 23 Oct 2014
