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 the&n...2228 days ago
“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
...useful information from RepeatMasker about transposable elements, retrieve their...nto complete TE copies, including LTR-retrotransposon Retrieve corresponding TE...ed library Allow for working with only a user-chosen set of TE families htt...2226 days ago
EAGLER: a scaffolding tool for long reads.
...e long reads are used to extend the contigs present in the NGS draft and possibly join overlapping contigs...th PacBio and Oxford Nanopore reads. The tool should be compatible with most UNIX flavors and has been su...2226 days ago
PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++.
...rategy that it implements for genome assembly: PRICE uses paired-read information to iteratively increase the size of existing contigs. Initially, those contigs can be individual re...2219 days ago
npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads
npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for micro...2219 days ago
2219 days ago
P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
...ter this tool was applied to scaffolding human contigs, the structures of both protein-coding genes and circular RNAs were almost completely recovered and equivalent to those in a complete genome, especi...2218 days ago
RestrictionDigest: A powerful Perl module for simulating genomic restriction digests
...e digestion and size selection process. It can also analyze multiple genomes at one run and generates concise comparison of enzyme(s) performance across the genomes. For more inf...2218 days ago
2216 days ago
SALSA: A tool to scaffold long read assemblies with Hi-C
...ands: cd SALSA make To run the code, you will need Python 2.7, BOOST libraries and Networkx(versi...and Koren, S., 2018. Integrating Hi-C links with assembly graphs for chromosome-scale assembly. bioRxiv, p...2215 days ago