2177 days ago
MCMCTREE: a phylogenetic program for Bayesian estimation of species divergence times
MCMCTREE is a phylogenetic program for Bayesian estimation of species divergence times using soft fossil constraints under various molecular clock models. This is part of...2175 days ago
HALC: High throughput algorithm for long read error correction
HALC, a high throughput algorithm for long read error correction. HALC aligns t...6.7-41.1% higher throughput than the existing algorithms while maintaining comparable...7% longer assembled contigs than the existing algorithms.2169 days ago
Many-to-many pairwise alignments of two sequence sets
needleall reads a set of input sequences and compares them...s to file. It uses the Needleman-Wunsch alignment algorithm to find the optimum alignment...) of two sequences along their entire length. The algorithm uses a dynamic programming me...2158 days ago
Circlator: automated circularization of genome assemblies using long sequencing reads
A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies u...2193 days ago
DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications
we propose a heuristic algorithm, called DUPCAR, for reconstructing ancestral...relationships in the ancestor. Then a greedy algorithm is used to reconstruct the an...Computer simulation was used to validate the algorithm. We also applied the method t...2187 days ago
2184 days ago
SALSA: A tool to scaffold long read assemblies with Hi-C
This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old v...2162 days ago
ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
With increased availability of de novo assembly algorithms, it is feasible to study ent...of non-model organisms. While algorithms are available that are speci...elop a transcriptome assembly algorithm that recovers alternatively s...e program that implements the algorithm is available at: http://facul...2144 days ago
2144 days ago