DendroPy: a Python library for phylogenetic computing
DendroPy is a Python library for phylogenetic computing. It provides cla...e reading and writing of phylogenetic data in a range of formats, such a...eful phylogenetic operations, such as data conversion and tree posterior...documentation . Descriptions of data for...2262 days ago
ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.
ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set. Detail paper at https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-82255 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 Pac.... After the initial assembly, Flye performs an extra repeat classification and analysis step to improve the structura...2251 days ago
MITObim - mitochondrial baiting and iterative mapping
This document contains instructions on how to use the MITObim pipeline described in Ha...ine was originally developed for Illumina data, but thanks to the versatilit...MIRA assembler, MITObim supports in principle also data fro...2247 days ago
MIX: Combining multiple assemblies from NGS data
Mix is a tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome...2247 days ago
kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity
The k-mer Weighted Inner Product. This software implements a de novo, alignment free measure of sample genetic d...g one. De novo estimates of genetic relatedness from next-gen sequencing data htt...2226 days ago
SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms
SEX-DETector is a probabilistic method that relies on RNAseq data from a cross (parents and progeny of each sex) to infer autosomal and...ot require prior sequencing of a reference genome: the same sequencing data can...2225 days ago
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Ranbow: a haplotype assembler for polyploid genomes
Ranbow is a haplotype assembler for polyploid genomes. It has been developed for th...haplotypes by gold standard (long) reads ranbow phylo: for the phylogenetic analysis...2223 days ago
Gblocks: eliminates poorly aligned positions and divergent regions of a DNA or protein alignment
Gblocks eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis. This server implements the m...2222 days ago