MCMCTREE: a phylogenetic program for Bayesian estimation of species divergence times
...REE 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 PAM...2179 days ago
SWALO: Scaffolding with assembly likelihood optimization
SWALO (scaffolding with assembly likelihood optimization) is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing. Please email your questions, comments, suggestions, and bug reports to atif.bd@gmail.com.2161 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
...wo technologies. Results: We designed and developed Hercules, the first machine learning-based long read error correction algorithm. The algorithm models every long read as a profile...2100 days ago
STRUM: structure-based prediction of protein stability changes upon single-point mutation
...ls of sequence and structure properties. The unique characteristics of STRUM is the combination of sequence profiles with low-resolution structure models from protein structure predic...2079 days ago
MimicrEE2: Genome-wide forward simulations of Evolve and Resequencing studies
...omic resources, supports biological particulars of model organism frequently used in E&R studies and offers a wide range of different adaptive models (selective sweeps, polygenic...2061 days ago
FRODOCK 2.0: fast protein–protein docking server
...t includes a complementary knowledge-based potential. The web interface provides a very effective tool to explore and select protein–protein models and interactively screen them...2042 days ago
2034 days ago
Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads
Deepbinner is a tool for demultiplexing barcoded Oxford Nanopore sequencing reads. It does this with a deep convolutional neural network classifier,...2001 days ago
HipSTR: Haplotype inference and phasing for Short Tandem Repeats
...h these errors in the hopes of obtaining more robust STR genotypes. In particular, it accomplishes this by: Learning locus-specific PCR stutter models using an EM algorithm M...1900 days ago
MSAProbs - Parallel and accurate multiple sequence alignment
...ate-of-the-art multiple sequence alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to ca...1776 days ago