WhatsHap: fast and accurate read-based phasing
WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for lo...2197 days ago
Porechop: tool for finding and removing adapters from Oxford Nanopore reads
Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its...2197 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 locate...2195 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 or protein alignment so that it becomes more suitable for phylogenetic analysis. This...2193 days ago
MCMCTREE: a phylogenetic program for Bayesian estimation of species divergence times
...m for Bayesian estimation of species divergence times using soft fossil constraints under various molecular clock models. This is part of the PAML package. In this tutoria...2193 days ago
CGView - Circular Genome Viewer
...e information and rendering options are supplied to the program using an XML file, a tab delimited file, o...he CGView gallery. http://wishart.biology.ualberta.ca/cgview/gallery.html http://stothard.afns.ualbe...2174 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once data formatting tools written in Perl. Headline Features: Fast, s...2165 days ago
ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
...y. Availability – A software program that implements the algorithm is available at: http://faculty.cse.tamu.edu/shsze/asplice. Sze SH, Pimsler ML, Tomberlin JK, Jones CD, Taro...2162 days ago
Epiviz: an interactive visualization tool for functional genomics data.
...lugin framework so users can addd3 visualizations. You can see a video tour here. https://bioconductor.org/packages/release/bioc/html/epivizr.html https://github.com/epiviz h...2156 days ago
Nanopolis: polish a genome assembly
...spect to a reference genome and more (see Nanopolish modules, below). Quickstart http://nanopolish.readthedocs.io/en/latest/quickstart_consensus.html Algorithms http://simpsonla...2139 days ago