Pash 3.0 performs sequence comparison and read mapping and can be employed as a module within diverse configurable analysis pipelines, including ChIP-Seq and methylome mapping by whole-genome bisulfite sequencing
SHORTY is targetted for de novo assembly of microreads with mate pair information and sequencing errors. SHORTY has some novel approach and features in addressing the short read assembly problem..
GUI for processing SAM/BAM and BED files. The software allows users to accurately estimate gene expression scores using short reads originating from both exons and exon-exon junctions, to generate wiggle files for visualization in UCSC genome browser, and to generate an alignment statis...
V-Xtractor uses Hidden Markov Models to locate, verify, and extract defined hypervariable sequence segments (V1-V9) from bacterial, archaeal, and fungal small-subunit rRNA sequences.
Tracembler streamlines the process of recursive database searches, sequence assembly, and gene identification in resulting contigs in attempts to identify homologous loci of genes of interest in species with emerging whole genome shotgun reads. A web server hosting Tracembler is provide...
Our algorithm uses a non-homogeneous hidden Markov model (HMM) that employs local recombination rates to identify chromosomal regions that are identical by descent (IBD=2) in children of consanguineous or non-consanguineous parents solely based on genotype data of siblings derived from ...