ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel...ne tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based...2279 days ago
REGEN: Ancestral Genome Reconstruction for Bacteria
REGEN infers evolutionary events, including gene creation and deletion and replicon fission and f...aximum parsimony or a maximum likelihood method. Gene content reconstruction is based on the concept of neighboring gene pairs...2264 days ago
alienness : Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life
Horizontal gene transfer (HGT) is the transmission of genes between organisms by other means than parental to offspring inheritance. While it is prevalent in prokaryotes, HGT is less...2258 days ago
EvidentialGene: tr2aacds, mRNA Transcript Assembly Software
EvidentialGene is a genome informatics project, "Evidence Directed Gene Construction for Eukaryotes",...struct high quality, accurate gene sets for animals and plants,...rsity, seehttp://arthropods.eugenes.org/EvidentialGene/Construct...e, combining all evidence for genes, from expressed sequences, g...2201 days ago
GLEAN: an unsupervised learning system to integrate disparate sources of gene structure evidence
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 training.2176 days ago
MCMCTREE: a phylogenetic program for Bayesian estimation of species divergence times
MCMCTREE is a phylogenetic program for Bayesian estimation of species divergence times using soft fossil constraints under various molecular clock models. This is pa...2176 days ago
BEAP: Blast Extension and Assembly Program
The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segme...2167 days ago
npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads
npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run...de, it can be integrated with simple structural analyses such as gene order...2167 days ago
2197 days ago
chromoMap-An R package for Interactive Visualization and Annotation of Chromosomes
...f any living organism allowing users to map chromosome elements (like genes, SNPs etc.) on the chromosom...nts, can visualize the data associated with chromosome elements (like gene expression) in the form of heat colors w...1862 days ago