An Introduction to Applied Bioinformatics
...;Caporaso Lab at Northern Arizona University. You can find information on the courses I teach on my teaching website and information on my research and lab on&nbs...2269 days ago
ARCS: scaffolding genome drafts with linked reads
ARCS, an application that utilizes the barcoding information contained in linked reads to further organize dra...ta. We expect ARCS to have broad utility in harnessing the barcoding information contained in linked read data...2265 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.2258 days ago
d3Network:Tools for creating D3 JavaScript network, tree, dendrogram, and Sankey graphs from R.
...twork package makes it easy to create these network graphs from R. The main idea is that you should able to take an R data frame with information about the relationships betwe...2234 days ago
G-compass: a comparative genome browser
...er 12 vertebrates based on original genome alignments pursuing higher coverage (1,2). Annotations of human genes/transcripts and their ortholog information were derived from H-InvD...2228 days ago
DendroPy: a Python library for phylogenetic computing
...n DendroPy 4.x runs under Python 3 (all versions > 3.1) and Python 2 (Python 2.7 only). You can install DendroPy by running: More information is available here: http://de...2217 days ago
Gblocks: eliminates poorly aligned positions and divergent regions of a DNA or protein alignment
...ged in the stand-alone program. You can see here an example output file showing the blocks selected from a protein alignment. Further information can be found in the onli...2177 days ago
“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
One code to find them all is a set of perl scripts to extract useful information from RepeatMasker about trans...posable elements, retrieve their sequences and get some quantitative information. Assemble RepeatMasker hit...2176 days ago
PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++.
..., a de novo genome assembler implemented in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read information to iteratively increase the s...2169 days ago
RestrictionDigest: A powerful Perl module for simulating genomic restriction digests
...n simulate the reference genome digestion and generate comprehensive information of the simulation. It can sim...comparison of enzyme(s) performance across the genomes. For more information, please see the academic pape...2167 days ago