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Duroc × Landrace × Large White pig is a crossbred species

• Resource
• SciCrunch
• 9 years ago - submitted by Kan Gao

One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide.. Regist custom genome software registers custom genomes to Genome Explorer (IN: FASTA).

• Resource
• RRID-Legacy
• 9 years ago - submitted by Sonoko Kinjo

One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide. loadGtfToGe_db software loads GTF files to a database for Genome Explorer. It allows the user to browse the results through the GE.

• Resource
• RRID-Legacy
• 9 years ago - submitted by Sonoko Kinjo

One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide. loadGffToGe_db for custom genome software loads GFF files of custom genomes to a database for Genome Explorer. It allows the user to browse the results through the GE.

• Resource
• RRID-Legacy
• 9 years ago - submitted by Sonoko Kinjo

One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide. loadBED2ge_db software is for visualizing mapping data by Genome Explorer on the web.

• Resource
• RRID-Legacy
• 9 years ago - submitted by Sonoko Kinjo

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software to predict the location of ribosomal RNA genes in genomes. It supports bacteria, archaea, mitochondria, and eukaryotes. It takes FASTA DNA sequence as input, writes GFF3 as output, and supports multithreading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

• Resource
• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software for sequence alignments that displays multiple match sequences aligned against a single genomic reference sequence. It can be used for manipulation, display and annotation of genomic data, to check the quality of an alignment, to find missing/misaligned sequence, and to identify splice sites and polyA sites.

• SciCrunch
• 9 years ago - submitted by Isabella Froman

Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software for clustering and assembling short reads, especially for RAD-seq. (restriction-site associated DNA sequencing).

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.

• Resource
• SciCrunch
• 9 years ago - submitted by Isabella Froman

THIS RESOURCE IS NO LONGER IN SERVICE. Documented January 29, 2018.<br/>From website: "Note that the eXpress software is also no longer being developed. We recommend you use kallisto instead." Kallisto can be found at http://pachterlab.github.io/kallisto/.<br/><br/>Software for streaming quantification for high-throughput DNA/RNA sequencing. <br/>Can be used in any application where abundances of target sequences need to be estimated from short reads sequenced from them.

• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software for multiple sequence alignment viewing, editing and phylogeny. It includes a set of user-configurable modes to color residues used to create high-quality reference alignments.

• Resource
• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software package to perform Bayesian analysis of molecular sequences using a family of Markov Chain Monte Carlo (MCMC) algorithms. It can estimate phylogenies using a wide range of models.

• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies.

• Resource
• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software for molecular visualization and modeling. It provides fast OpenGL-based visualization of molecular structures, molecular mechanics methods (minimization, MD simulation using the AMBER, CHARMM, and MMFF94 force fields), calculation and visualization of electrostatic properties (FDPB) and molecular editing features.

• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software toolkit for multispecies target DNA enrichment probe design. It consists of two programs: BaitFisher and BaitFilter, which are designed to construct hybrid enrichment baits for multiple sequence alignments or annotated features in multiple sequence alignments.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software for sequencing data analysis and demultiplexing. It can be used in situations where sequence reads contain the barcodes that uniquely distinguish samples.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.

• SciCrunch
• 9 years ago - submitted by Isabella Froman

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software for automated docking analysis to precalculate the set of grids describing the target protein. It is a part of automated molecular modeling simulation software AutoDock.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software for gene prediction in eukaryotic genomic sequences. Serves as a basis for further steps in the analysis of sequenced and assembled eukaryotic genomes.

• Resource
• SciCrunch
• 9 years ago - submitted by Isabella Froman