2246 days ago
HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
...others. With this in mind, HapCUT2 is designed for speed and accuracy across diverse sequencing technolog...limited to: NGS short reads (Illumina HiSeq) clone-based sequencing (Fosmid or BAC clones) SMRT reads...2246 days ago
DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications
we propose a heuristic algorithm, called DUPCAR, for reconstructing ancestral genomic or...te the algorithm. We also applied the method to reconstruct the ancestral chromosome X of placental mammals and...2240 days ago
bpRNA: large-scale automated annotation and analysis of RNA secondary structure
...g RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with the positions, sequence, and flanking...2238 days ago
2237 days ago
WhatsHap: fast and accurate read-based phasing
...even “complex” variants (such as TCG → AGAA) Pedigree phasing mode uses reads from related individuals (such as trios) to improve results and to re...2233 days ago
SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms
...s 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 on the non recombining part of sex chromosomes). How does SEX-DETector...2231 days ago
CrossMap: a program for convenient conversion of genome coordinates
CrossMap is a program for convenient conversion of genome...9 (MGSCv37) <> mm10 (GRCm38)). It supports most commonly used file formats i...ding SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF. CrossMap is designed to liftover g...2230 days ago
2230 days ago
Gblocks: eliminates poorly aligned positions and divergent regions of a DNA or protein alignment
Gblocks eliminates poorly aligned positions and divergent regions of a DNA o...ylogenetic analysis. This server implements the most important features of the Gblocks program to make its use as simple as possible without loosing the func...2228 days ago