DendroPy: a Python library for phylogenetic computing
...ng some useful phylogenetic operations, such as data conversion and tree posterior distribution summarizat...orials and documentation, is at: http://dendropy.org/ DendroPy is also hosted in the official Python rep...2265 days ago
D3 javascript for visualization !
Welcome to the D3 gallery! More examples are available on bl.ocks.org/mbostock. If you want to share an example and don't have your own hosting, consider using Gist and bl.ocks.org. If you want to share or view live examples try vida.io.2265 days ago
NGMLR: long-read mapper designed to align PacBio or Oxford Nanopore
CoNvex Gap-cost alignMents for Long Reads (ngmlr) is...orrectly align the reads, including those spanning (complex) structura...l alignment. Ngmlr uses a convex gap cost model that penalizes gap ext...ve at more precisely identifying the position of breakpoints stemming...2263 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 to find the overlaps be...2253 days ago
Metassembler: merging and optimizing de novo genome assemblies
...of the individual assemblies. Genome assembly projects typically run multiple algorithms in an attempt to find the single best assembly, although those assemblies often have comple...2250 days ago
MIX: Combining multiple assemblies from NGS data
...draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extensi...2250 days ago
MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error corre...2247 days ago
LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
...thod that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo ge...ton JN#, Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J#. Chromosome-scale scaffolding of de no...2244 days ago
fragScaff: Genome Assembly with Contiguity Preserving Transposition
Contiguity preserving transposition and sequencing (CPT-seq) is an entirely in...ange contiguity to support robust, accurate chromosome-scale de novo genome assem...nformation for de novo genome assembly via transposase contiguity. Genome Re...2244 days ago
GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads
...you use this program in a publication, please cite the following reference:Chong Chu, Xin Li, and Yufeng Wu. "GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with...2244 days ago