Search Results for "swing java" - Page 5

ScreeningAssistant 2 is a modular software dedicated to perform various simple and advanced chemoinformatics analysis around chemical libraries.

FastMap is Java based software that performs quantitative trait locus mapping for gene expression data (eQTL Mapping).

iPiG targets the integration of peptide spectrum matches (PSMs) from mass spectrometry (MS) peptide identifications into genomic visualisations provided by genome browser such as the UCSC genome browser (http://genome.ucsc.edu/). iPiG takes PSMs from the MS standard format mzIdentML (*.mzid) or in text format and provides results in genome track formats (BED and GFF3 files), which can be easily imported into genome browsers. For more details about iPiG and it's functionallity, please...

The Blast2SNP is able to pick out synonymous, non-synonymous mutations and indels from draft assembly sequences by performing BLAST search against the reference ORF sequences.

Pontos is an easy-to-use, graphical Java program for the calculation of uncorrected distance (or similarity) matrices from DNA sequence alignments in PHYLIP format. It also creates "difference" alignments from regular ones (and vice-versa). It can handle gaps and ambiguities in different ways. Gaps can be: - all used; - all ignored; - ignored only at the ends of the sequences, in a pairwise manner; - ignored only at the ends, but now globally (in effect trimming the whole alignment...

JFinisher is software for alignment, editing and manipulation of biological sequences. It aims to assist in the finishing of genome assembly. Starting from a reference sequence, the program align contigs using Smith-Waterman local alignment algoritm with auxiliary methods, allowing management of the alignments generated. It has graphical interface for manipulation and visualization of the actions, uniting features that help in editing the sequences. It has internal projects manageable and...

Phenex is an application for annotating taxa and phenotypes in character matrix files with ontology terms. Phenex saves ontology annotations alongside traditional character matrix data using the NeXML format standard for evolutionary data. Current Phenex development is taking place at GitHub: https://github.com/phenoscape/Phenex

Alignment of the assembled sequences to a reference genome is a common way to obtain a likely order for the contigs, though most of times the final decision is taken by the user. We present the jContigSort, a tool that sorts the genome contigs.

OrthoInspector is a new software system for orthology/paralogy analysis. Its purpose is to facilitate the installation and the maintenance of a database describing orthology/inparalogy relations and to provide tools to exploit these data.

A Generalized Combinatorial Approach for Detecting Gene-by-Gene and Gene-by-Environment Interactions

iso2l (ˈaisəutuːl, spoken isotool) is a software to calculate the isotopic distribution of a chemical formula or a amino acid chain. The development has been MOVED TO https://github.com/binfalse/iso2l

A plugin for the VANTED system, called Glyph-based Link Exploration of Pathways (GLIEP). It helps to guide the navigation and exploration process of interconnected pathway visualization as well as insight into the overall interconnectivity.

BAMStats is a GUI desktop tool for calculating and displaying metrics to assess the success of Next Generation Sequencing mapping tools. BAMstats is written in Java and based around the Picard API.

Graphical User Interface for a software used to assess adaptive evolution in protein-coding genes. Makes use of several known bioinformatics software. IMPACT is free software, targeted to the scientific community. Maldonado E, Dutheil JY, da Fonseca RR, Vasconcelos V, Antunes A (2011) IMPACT: Integrated Multiprogram Platform for Analyses in ConTest. Journal of Heredity, 102 (3): 366-369. doi: https://doi.org/10.1093/jhered/esr003

A computational tool to design and annotate metabolic pathways from genome annotations

The Katsura tool overlays microarray gene expression data, proteomics, and similar biological data onto metabolic pathways. [Pathogen Functional Genomics Resource Center (PFGRC) @ J. Craig Venter Institute (JCVI)]

PAICE is a rapid bioinformatics pathway visualization tool for KEGG-compatible accessions derived from Illumina Solexa next-gen and Affymetrix datasets. It colors KEGG pathways while appreciating detection-calls and duplicate gene copies.

VELMA stands for Visualization & Exploration of Large Multiple sequence Alignments. VELMA is a Java tool for visualizing alignments of large numbers of biological sequences that exceed the capabilities of existing software.

The program versusSNP is a flexible tool for mining SNPs between two close related genomes. First, we align all the orthologous genes and select SNPs, then the SNPs are separated into categories based on their mutation types.

MSA2SNP is a tool for mining SNP sites in multiple sequence alignment (MSA). This tool inherits the easy-to-use interface from MEGA4 Explorer with advance data presentation. MSA2SNP lets you visualize alignments and import from CLUSTAL program directly.

3D Genome Tuner draws circular genome map and enables viewing multi-genomes in 3D context. It also provides genome analysis and sequence alignment, making it a powerful tool in genome studies and demonstrations.

Software environment for manipulation of DNA and protein sequences in a phylogenetic context.

The final build of this software now is distributed in R, embedded in "RedeR': an R/Bioconductor package for hierarchical and nested network analysis... more about RedeR: http://bioconductor.org/packages/2.9/bioc/html/RedeR.html

RssGsc (Rank Sum Statistics for Gene Set Collections) is a bioinformatics tool used to find meaningful gene sets using a ranked list of genes (obtained form an experiment).

PhyloSort sorts phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units.