SMASH: An alignment-free tool to find and visualise rearrangements between pairs of DNA sequences
SMASH is a completely alignment-free method to find and visualise rearrangements between pairs of DNA sequen..., also known as Markov model, of high context order (typically 20). The method has been approached with a to...2354 days ago
Dot, an interactive viewer for genome-genome comparison
...lies and perform exploratory comparative genomics. Dot supports the output of MUMmer’s nucmer aligner the most commonly used software method for aligning genome assemblie...2330 days ago
2298 days ago
REGEN: Ancestral Genome Reconstruction for Bacteria
...e creation and deletion and replicon fission and fusion. The reconstruction can be performed by either a maximum parsimony or a maximum likelihood method. Gene content reconstruction...2280 days ago
Multi-CAR: a tool of contig scaffolding using multiple references
we design a simple heuristic method to further revise our single reference-based scaffolding tool CAR into a new one called Multi-CAR such that it can utilize multiple complete genom...2279 days ago
Reference-free prediction of rearrangement breakpoint reads
...r, evaluation on a real prostate cancer dataset shows that the proposed method predicts more fusion transcri...roduces fewer false-positive reads. To our knowledge, this is the first method to detect breakpoint reads wi...2278 days ago
SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms
SEX-DETector is a probabilistic method that relies on RNAseq data from a cross (parents and progeny of each sex) to infer autosomal and sex-linked genes (genes located on the non reco...2194 days ago
MCMCTREE: a phylogenetic program for Bayesian estimation of species divergence times
...I will analyze an easy example modified from dataset of Inoue et al. (2010). Here we conduct a commonly used time estimation method, "Approximate Likelihood Method", for the datasets including...2192 days ago
Cerulean: A hybrid assembly using high throughput short and long reads
...Illumina paired-end reads using long reads like PacBio RS long reads. Cerulean v0.1 has been implemented with bacterial genomes in mind. The method is fully described in Deshpan...2188 days ago
2181 days ago