SMASH: An alignment-free tool to find and visualise rearrangements between pairs of DNA sequences
SMASH is a completely alignment-free method to find and visualise rearrangements between pairs of DNA sequences. Th...ction is based on relative compression, namely using a FCM, also known as Markov...2343 days ago
Alien_Hunter : prediction of putative Horizontal Gene Transfer (HGT) events
Alien_hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the impl...r methods. Optionally the predictions can be parsed into a 2-state 2nd order Hidden Markov...2326 days ago
mojolicious: a next generation web framework for the Perl programming language.
Back in the early days of the web, many people learned Perl because of a wonderful Perl libra...selector support. Very clean, portable and object-oriented pure-Perl API with no hidden...2321 days ago
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
ETE v3, featuring numerous improvements in the underlying library of methods, and pro...hylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distance...2283 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 the PAM...2180 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.2163 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
...ts: We designed and developed Hercules, the first machine learning-based long read error correction algorithm. The algorithm models every long read as a profile Hidden Markov Model with respect to the und...2101 days ago
STRUM: structure-based prediction of protein stability changes upon single-point mutation
STRUM is a method for predicting the fold stability change (ΔΔG) of prote...of STRUM is the combination of sequence profiles with low-resolution structure models from protein structure predic...2080 days ago
MimicrEE2: Genome-wide forward simulations of Evolve and Resequencing studies
MimicrEE2, a multi-threaded Java program for genome-wide forward simulations of evolv...equently used in E&R studies and offers a wide range of different adaptive models (selective sweeps, polygenic...2062 days ago
FRODOCK 2.0: fast protein–protein docking server
frodock: a user-friendly protein–protein docking server based on an improv...ace provides a very effective tool to explore and select protein–protein models and interactively screen them...2043 days ago