SMASH: An alignment-free tool to find and visualise rearrangements between pairs of DNA sequences
...alise rearrangements between pairs of DNA sequences. The detection is based on relative compression, namely using a FCM, also known as Markov model, of high context order (typic...2342 days ago
PASA: Gene Structure Annotation and Analysis
...ble Spliced Alignments, is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maint...2336 days ago
Alien_Hunter : prediction of putative Horizontal Gene Transfer (HGT) events
...e 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...2324 days ago
PSPairwise Sequentially Markovian Coalescent (PSMC) model
Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model2223 days ago
NGMLR: long-read mapper designed to align PacBio or Oxford Nanopore
...algorithm to compute the final alignment. Ngmlr uses a convex gap cost model that penalizes gap extensions...gaps less than for shorter ones to compute precise alignments. The gap model allows ngmlr to account for b...2217 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...2181 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.2179 days ago
2176 days ago
ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
...sembly algorithms, it is feasible to study entire transcriptomes of non-model organisms. While algorithms a...nd memory-efficient algorithm for de novo transcriptome assembly of non-model organisms. BMC Genomics 18(Su...2148 days ago
RNA-seq Analysis Workshop Course Materials
...inst the reference genome and significantly improves our ability to reconstruct transcripts. This category would obviously include humans and most model organisms but excludes the ma...2148 days ago