Delta: a new Web-based 3D genome visualization and analysis platform
Delta is an integrative visualization and analysis pl...oops in the genome. It then generates a physical 3D model which represents the plausibl...h extensive genome annotation by juxtaposing the 3D model with diverse genomic assay ou...2321 days ago
Meraculous: Haplotype-sensitive Assembly of Highly Heterozygous genomes.
Meraculous is a whole genome assembler for Next Generation Sequencing data geared for...under a day. The process pipeline implements a highly transparent and portable model of job control and monitoring...2321 days ago
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 bet...tion is based on relative compression, namely using a FCM, also known as Markov model, of high context order (typic...2320 days ago
PASA: Gene Structure Annotation and Analysis
PASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome anno...exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maint...2314 days ago
Alien_Hunter : prediction of putative Horizontal Gene Transfer (HGT) events
...ably the local composition of a sequence compared to fixed-order methods. Optionally the predictions can be parsed into a 2-state 2nd order Hidden Markov Model (HMM), in a change-point dete...2303 days ago
mojolicious: a next generation web framework for the Perl programming language.
Back in the early days of the web, many people learned Perl because of a wonderful Perl libra...selector support. Very clean, portable and object-oriented pure-Perl API with no hidde...2298 days ago
PSPairwise Sequentially Markovian Coalescent (PSMC) model
Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model2201 days ago
NGMLR: long-read mapper designed to align PacBio or Oxford Nanopore
CoNvex Gap-cost alignMents for Long Reads (ngmlr) is a lon...e the final alignment. Ngmlr uses a convex gap cost model that penalizes gap extensions...shorter ones to compute precise alignments. The gap model allows ngmlr to account for b...2195 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...2160 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.2157 days ago