LSGSP is the java codes which provided for use on this site are not part of the book Large-Scale Genome Sequence Processing published by Imperial College Press
JolyTree implements an alignment-free distance-based procedure for inferring phylogenetic trees from genome contig sequences. For each pair of genomes, a dissimilarity measure is first computed and next transformed to obtain an estimation of the number of substitution events that have occurred during their evolution.
Hobbes is a software package for efficiently mapping DNA snippets (reads) against a reference DNA sequence. It can map short and long reads, and supports Hamming distance (only substitutions) and edit distance (substitutions/insertions/deletions). Hobbes accepts both single-end and paired-end reads for alignment, and can run on multiple CPU cores using multithreading.
::DEVELOPER
CBCL Lab (Computational Biology and Computational Learning) @ UCI
perEditor (Personal Genome Editor) changes the reference human genome (NCBI36/hg18) into an individual genome, taking into account single nucleotide polymorphisms (SNPs), insertions and deletions, copy number variation, and chromosomal rearrangements. perEditor outputs two alleles (maternal, paternal) of the individual genome that is ready for mapping ChIP-seq and RNA-seq reads, and enabling the analyses of allele specific binding, chromatin structure, and gene expression.
Atlas-Link links and orients genome sequence contigs into scaffolds quickly and accurately using mate-pair information. Atlas-Link can also be used to superscaffold existing genome assemblies with data from new sequencing technologies.
GenePalette allows genome sequence visualization and navigation. Users can download from NCBI’s GenBank database large or small segments of genome sequence from a variety of organisms preserving the gene annotation that is associated with that sequence. Sequence elements of interest (transcription factor binding sites, etc. can be searched for and identified in the loaded sequence, and then clearly visualized within a colorful graphical representation of gene organization.