PhyloGrapher - Graph Visualization Tool
PhyloGrapher is a program designed to visualize and study evolutionary relationships within families of homologous genes or proteins (elements). PhyloGrapher is a drawing tool that generates custom graphs...2262 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. The algorithm uses an A-Bruijn graph...2204 days ago
2204 days ago
HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
HISAT2 is a fast and sensitive alignment program for mapping next-ge...me). Based on an extension of BWT for graphs [Sirén et al. 2014], we designed and implemented a graph FM index (GFM), an original a...exing scheme is called a Hierarchical Graph...2201 days ago
MIX: Combining multiple assemblies from NGS data
Mix is a tool that combines two or more draft assemblies, without relying on a referenc...nishing. The proposed algorithm builds an extension graph where vertices represent extr...put assembly corresponds to a path in the extension graph...2201 days ago
2194 days ago
TULIP - The Uncorrected Long read Integration Pipeline
TULIP currently consists of two Perl scripts, tulipseed.perl and tulipbulb.perl. These are very much intended as p...s as input alignments files of long reads to sparse short seeds, and outputs a graph...2194 days ago
bpRNA: large-scale automated annotation and analysis of RNA secondary structure
bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to...h such structural feature. The bpRNA code is written in perl and requires the Graph...2186 days ago
2145 days ago
ReMILO: reference assisted misassembly detection algorithm using short and long reads.
ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads...n constructs a novel data structure called red-black multipositional de Bruijn graph...2142 days ago