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REVIGO: Reduced Visualize gene ontology
By Jit 2776 days agohttp://revigo.irb.hr/ - REViGO can take long lists of Gene Ontology terms and summarize them by removing redundant GO terms. The remaining terms can be visualized in semantic similarity-based scatterplots, interactive graphs, or tag clouds. More about...GeneMates: an R package for Detecting Horizontal Gene Co-transfer between Bacteria Using Gene-gene...
By Rahul Nayak 2191 days agogithub.com - GeneMates is an R package implementing a network approach to identify horizontal gene co-transfer (HGcoT) between bacteria using whole-genome sequencing (WGS) data. It is particularly useful for investigating intra-species HGcoT, where...G-NEST: The Gene NEighborhood Scoring Tool
By Neel 1988 days agogithub.com - The Gene NEighborhood Scoring Tool (G-NEST) combines genomic location, gene expression, and evolutionary sequence conservation data to score putative gene neighborhoods across all window sizes. Primary author of final code = William F. Martin....Tigers genome sequenced
By Rahul Agarwal 4554 days agoOnly 4.4 percent DNA difference between Tiger and house catsGLEAN: an unsupervised learning system to integrate disparate sources of gene structure evidence
By Poonam Mahapatra 2835 days agosourceforge.net - GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior...GeneOverlap: An R package to test and visualize gene overlaps
By Jit 2626 days agobioconductor.org - Overlapping gene lists can reveal biological meanings and may lead to novel hypotheses. For example, histone modification is an important cellular mechanism that can pack and re-pack chromatin. By making the chromatin structure more dense or loose,...PyParanoid: a pipeline for rapid identification of homologous gene families in a set of genomes
By BioStar 2032 days agogithub.com - PyParanoid is a pipeline for rapid identification of homologous gene families in a set of genomes - a central task of any comparative genomics analysis. The "gold standard" for identifying homologs is to use reciprocal best hits (RBHs) which depends...Mercator: Multiple Whole-Genome Orthology Map Construction
By Jit 2118 days agowww.biostat.wisc.edu - Whole-genome homology maps attempt to identify the evolutionary relationships between and within multiple genomes. The term "syntenic" is often used to describe regions of multiple genomes that are believed to have evolved from the same region in an...DendroPy: a Python library for phylogenetic computing
By Seema Singh 2875 days agopypi.org - DendroPy is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a...
