phyloXML: XML for evolutionary biology and comparative genomics
...nd identifiers, branch lengths, support values, and gene duplication and speciation events. Using these standardized elements allows interoperability between various appli...2411 days ago
PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool
...ue software architecture, PLAST takes full advantage of recent multi-core personal computers without requi...ence comparison tool providing the following benefits: PLAST is a high-performance sequence comparison...2410 days ago
dnaPipeTE: de-novo assembly & annotation Pipeline for Transposable Elements
dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and qu...n small datasets (< 1X). dnaPipeTE is developped by Clé...mples of quantification and TE landscape (relative age) produced by dn...2408 days ago
MetaSim A Sequencing Simulator for Genomics and Metagenomics.
...composition of typical metagenome data sets. Based on a database of given genomes, the program allows the user to design a metagenome by specifying the number of genomes...2406 days ago
Bandage: interactive visualization of de novo genome assemblies
...l for visualizing assembly graphs with connections. Users can zoom in to specific areas of the graph and i...g labels, changing colors and extracting sequences. BLAST searches can be performed within the Bandage gra...2406 days ago
HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. Since version 2.7.0, HiC-Pro supports the m...2405 days ago
COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping p...om Arabidopsis thaliana with 1% base error. COPE connected over 99% of reads w...han the recently published tool FLASH. When COPE is applied to real reads for...2405 days ago
Musket: a multistage k-mer spectrum based corrector
...quencing. This corrector employs the k-mer spectrum approach and introduces...rection techniques in a multistage workflow. Our performance evaluation results,...ed using a master-slave model and demonstrates superior parallel scalability comp...2405 days ago
ACANA: An accurate and consistent alignment tool for DNA sequences
ACANA is an accurate and consistent alignment tool for DNA sequences. ACANA is specifically designed for aligning sequences that share only some moderately conserved regions and/or...2404 days ago
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