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Software that predicts HLA haplotype by hierarchically weighting reads and using an iterative, greedy, top down pruning technique. HLAforest uses BioPerl to read in FASTA files. Alignments use Bow tie, although any alignment tool can be used to generate SAM alignments for use as input to HLAforest.

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• SciCrunch
• 12 years ago - by Anonymous

Software that can consistently estimate the topology and branch lengths (in coalescent units) of the species tree. Although the pseudo-likelihood is derived from coalescent theory, and assumes no gene flow or horizontal gene transfer (HGT), the MP-EST method is robust to a small amount of HGT in the dataset. In addition, increasing the number of genes does not increase the computational time substantially. The MP-EST method is fast for analyzing datasets that involve a large number of genes but a moderate number of species.

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• SciCrunch
• 12 years ago - by Anonymous

A software package of utilities for data extraction, quality control assessment, detection of overlapping and unique metabolites in multiple datasets, and batch annotation of metabolites. xMSanalyzer comprises of utilities that can be classified into five main modules: 1) merging apLCMS or XCMS sample processing results from multiple sets of parameter settings, 2) evaluation of sample quality, feature consistency, and batch-effect, 3) feature matching, and 4) characterization of m/z using KEGG REST; 5) Batch-effect correction using ComBat.

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• SciCrunch
• 12 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core facility provides consultancy services as well as contract work in all areas of bioinformatics, chemoinformatics and systems biology.

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• SciCrunch
• 14 years ago - by Anonymous

A bioinformatical software tool for analyzing (quantitative) phosphoproteome datasets. The program retrieves kinase-substrate predictions from NetworKIN and contains various statistical modules for futher analysis.

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• SciCrunch
• 12 years ago - by Anonymous

A Java-based standalone application for predicting both general and kinase-specific protein phosphorylation sites.

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• SciCrunch
• 12 years ago - by Anonymous

Software that predicts the wide selection of 88 different types of the single amino acid post-translational modifications (PTM) in protein sequences. The source code and precompiled binaries of brainstorming tool are available under Apache licensing.

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• SciCrunch
• 12 years ago - by Anonymous

Software for clustering time-evolving networks.

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• SciCrunch
• 12 years ago - by Anonymous

A computational software tool to predict leucine-rich nuclear export signals (NESs) by using profiles that had been further optimized by training and combining the amino acid properties of the NES-flanking regions. It is a multiplatform command-line Perl application with activity-based NES profiles.

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• SciCrunch
• 12 years ago - by Anonymous

Software that builds on probability theory to visualize significant conserved sequence patterns in multiple peptide sequence alignments against background (reference) sequence sets that can be tailored to the studied system and the used protocol.

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• SciCrunch
• 12 years ago - by Anonymous

A pipeline of software programs to design and analyze PCR primers. It is built in Python using the open-source PyCogent toolkit.

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• SciCrunch
• 12 years ago - by Anonymous

A python program that uses the polymorphism data obtained from mapping individual Illumina sequence reads onto a reference genome to identify polymorphic STRs.

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• SciCrunch
• 12 years ago - by Anonymous

A set of software tools to simplify the range of computational activities involved in regulatory network inference. It is technology-independent and includes an interface layer to allow easy integration of components into other applications. It is implemented in MATLAB and is available for all researchers to use.

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• SciCrunch
• 12 years ago - by Anonymous

A suite of python scripts to perform high-throughput investigation of RNA editing using next-generation sequencing data.

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• SciCrunch
• 12 years ago - by Anonymous

An alignment-free software tool which uses a computational pipeline based on an improved k-mer scheme and a support vector machine (SVM) algorithm to distinguish lncRNAs from messenger RNAs (mRNAs), in the absence of genomic sequences or annotations. It is especially suitable for PacBio or 454 sequencing data and large-scale transcriptome data.

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• SciCrunch
• 12 years ago - by Anonymous

A computational software tool for estimating linkage disequilibrium (LD) from pooled resequencing data.

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• SciCrunch
• 12 years ago - by Anonymous

Software that uses the genotype data in conjunction with the pooled sequence data in order to accurately estimate the proportions of the samples in the pool, even in cases where not all individuals in the pool were genotyped (eALPS-LD).

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• SciCrunch
• 12 years ago - by Anonymous

Software tool for inferring haplotypes from pooled sequencing. Enables to infer strain numbers and haplotype frequencies in silico from sequences of pooled samples.

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• SciCrunch
• 12 years ago - by Anonymous

Software that implements some population genetics tests and estimators that can be applied to pooled sequences from Next Generation Sequencing experiments.

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• SciCrunch
• 12 years ago - by Anonymous

A perl-based package to perform comparative analysis of metabolic pathways between two organisms.

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• SciCrunch
• 12 years ago - by Anonymous