DAGchainer: Computing Chains of Syntenic Genes in Complete Genomes
The DAGchainer software computes chains of syntenic genes found within complete genome sequences. As input, DAGchainer accepts a list of gene pairs with sequence homolog...2636 days ago
LoRDEC: a hybrid error correction program for long, PacBio reads
...c. Why is LoRDEC different? It is efficient and can process large read data sets, included from eukaryotic or vertebrate species, on a usual computing server, and even works on des...2584 days ago
ChromHMM: Chromatin state discovery and characterization
...nce of each chromatin mark. The resulting model can then be used to systematically annotate a genome in one or more cell types. By automatically computing state enrichments for large-s...2575 days ago
npScarf: Scaffolding and Completing Assemblies in Real-time Fashion
...carf) is a program that scaffolds and completes draft genomes assemblies in real-time with Oxford Nanopore sequencing. The pipeline can run on a computing cluster as well as on a lapto...2541 days ago
Omega2: metagenome assembly pipeline
...MiSeq 300-bp dataset. In comparison with Celera on the MiSeq dataset, Omega provided more continuous assemblies overall using a fraction of the computing time of existing overlap-layo...2493 days ago
Ra assembler - a de novo DNA assembler for third generation sequencing data
...ntegration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institu...2323 days ago
Seal: SEquence ALignment evaluation suite
...tandardized interface. Parsing the output of the alignment tool and calculating the number of reads that were correctly or incorrectly mapped. Computing run times and measures of acc...2316 days ago
DendroPy: a Python library for phylogenetic computing
DendroPy is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices...2206 days ago
ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
...NA-Seq libraries as possible that contain hundreds of gigabases of data. New techniques are developed so that computations can be performed on a computing cluster with moderate amount...2135 days ago
IQ-TREE: Efficient software for phylogenomic inference
...to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time IQ-TREE found higher li...1905 days ago