Jabba: Hybrid Error Correction for Long Sequencing Reads
...data. Input Jabba takes as input a concatenated de Bruijn graph and a set of sequences: the de Bruijn...ntry per node, the meta information should be in the format:>NODE the set of sequences should be in fas...2024 days ago
Frontend: Perl Web framework documentation - Andrej Sali Lab
The frontend is a set of Perl classes that displays the web interface, allowing a user to...eb service. This class is then used to display the web pages using a set of CGI scripts that are set up automatically by the build...2350 days ago
2333 days ago
2313 days ago
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylo...2309 days ago
REGEN: Ancestral Genome Reconstruction for Bacteria
...a maximum likelihood method. Gene content reconstruction is based on the concept of neighboring gene pairs. REGEN was designed to be used with any set of genomes that are sufficien...2294 days ago
PhyloGrapher - Graph Visualization Tool
...ships within families of homologous genes or proteins (elements). PhyloGrapher is a drawing tool that generates custom graphs for a given set of elements. In general, it i...2293 days ago
SCUBAT: Scaffolding Contigs Using Blat And Transcripts
SCUBAT (Scaffolding Contigs Using BLAT And Transcripts) uses any set of transcripts to identify cases where a transcript is split over multiple genome fragments and attempts to use this information to scaffold the genome.2287 days ago
ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.
ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set. Detail paper at https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-82239 days ago
2235 days ago