BOL

github.com - Cogent is a tool that identifies gene families and reconstructs the coding genome using high-quality transcriptome data without a reference genome, and can be used to check assemblies for the presence of these known coding...

bitbucket.org - TAndem REpeat ANalyzer -TAREAN – is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their...

www.softberry.com - FGENESH is the fastest (50-100 times faster than GenScan) and most accurate gene finder available - see the figure and the table below. In recent rice genome sequencing projects, it was cited "the most successful (gene finding) program (Yu et...

github.com - R Package to visualize alignments between two or multiple DNA sequences includinga number of functionalities to facilitate processing of alignments in PAF format. SVbyEye, an open-source R package to visualize and annotate sequence-to-sequence...

github.com - LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences. The Program first constructs all exact match pairs by a suffix-array based algorithm and extends them to long highly similar pairs. Then...

catchenlab.life.illinois.edu - Chromonomer is a program designed to integrate a genome assembly with a genetic map. Chromonomer tries very hard to identify and remove markers that are out of order in the genetic map, when considered against their local assembly order; and to...

bokeh.pydata.org - Bokeh is an interactive visualization library that targets modern web browsers for presentation. Its goal is to provide elegant, concise construction of versatile graphics, and to extend this capability with high-performance interactivity over very...

fantom.gsc.riken.jp - ZENBU is a data integration, data analysis, and visualization system enhanced for RNAseq, ChipSeq, CAGE and other types of next-generation-sequence-tag (NGS) based data. ZENBU allows for novel data exploration through "on-demand" data...

mulan.dcode.org - Mulan performs multiple (2 or more) sequence alignments with an efficient and rapid "full local" alignment strategy that ensures a recapitulation of evolutionary sequence rearrangements (such as inversions and reshuffling) in any of the species. It...

bioinformatics.um6p.ma - AlignStatPlot, a new R package and online tool that is well-documented and easy-to usefor MSA and post-MSA analysis. This tool performs both traditional and cutting-edge analy-ses on sequencing data and generates new visualisation methods for MSA...