phyloXML: XML for evolutionary biology and comparative genomics
phyloXML (example) is an XML language designed to describe phylogenetic trees (or networks) and associated data. PhyloXML provides elements for commonly used features, such as taxonomic information, gene nam...1653 days ago
StringTie Transcript assembly and quantification for RNA-Seq
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into pot...ipts representing multiple splice variants for each gene locus. Its input can include...eads. In order to identify differentially expressed genes be...1469 days ago
LibsDyogen: Libibrary for comparative genomics
Library of usual classes and functions written in python and used in the Dyogen team for comparative genomics applications. Collaborative python library used in the DYOGEN teamfor studying the evolution of gene order in vertebrates. http://www.ibens.ens.fr/?rubrique43&lang=fr1637 days ago
DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies
DeCoSTAR computes adjacency evolutionary scenarios using a scoring scheme based on a weighted sum of adjacency...minutes, DeCoSTAR can reconstruct the evolutionary history of domains inside genes, of gene fus...1627 days ago
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alien_index : identify potential contaminants or horizontally transferred genes in transcriptomes.
identify potential contaminants or horizontally transferred genes in transcriptomes. algorithm is based on alo...rithm described in the following: Gladyshev, Eugene A., Matthew Meselson, and Irina R. Arkhipova. "Massive horizontal gene tra...1597 days ago
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PANEV: an R package for a pathway-based network visualization
PANEV (PAthway NEtwork Visualizer) is an R package set for gene/pathway-based network visualization. Based on information available on KEGG, it visualizes genes within a network of multiple...interpret functional profiles of a cluster of genes....1590 days ago
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