PAired-eND Assembler for DNA sequences
PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. More at https://github.com/neufeld/pandaseq2963 days ago
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DeCoSTAR - Detection of Co-evolution
DeCoSTAR is a software which aims at reconstructing ancestral gene or genome organizations, in the form of set...sibility to handle badly assembled genomes. DeCoSTAR is able to reconstruct the histories of domains insi...2590 days ago
CABOG: Celera Assembler with Best Overlap Graph
...st to overcome the fundamental limitation of all sequencing machines, namely, that they read out very few DNA letters at a time. These programs reconstruct genomes that are billions of...2559 days ago
CAR: Reconstructing Contiguous Regions of an Ancestral Genome
...are reasonably accurate and that they will become highly accurate in the foreseeable future. Our methods were developed as part of a project to reconstruct the genome sequence of the la...2556 days ago
MGRA: Breakpoint graphs and ancestral genome reconstructions
...Rearrangements and Ancestors) is a tool for reconstruction of ancestor genomes and ev...y or partially, in the latter case MGRA can reconstruct conserved ancestral regions (...o have different gene content. It also can reconstruct most plausible phylogenetic t...2488 days ago
DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications
...e a heuristic algorithm, called DUPCAR, for reconstructing ancestral genomic orders w...ncestor. Then a greedy algorithm is used to reconstruct the ancestral orders by conne...he algorithm. We also applied the method to reconstruct the ancestral chromosome X of...2188 days ago
RNA-seq Analysis Workshop Course Materials
...r which an RNAseq experiment is performed. It allows reads to be aligned against the reference genome and significantly improves our ability to reconstruct transcripts. This category wo...2145 days ago