ermine Bio Modules 18.04

  • AlphaFold/2.2.2-foss-2021a-CUDA-11.3.1 AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known
  • Beast/1.10.5pre_thorney_v0.1.2-GCC-11.2.0 BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability.
  • Biopython/1.79-foss-2021a Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.
  • Eigen/3.3.9-GCCcore-11.2.0 Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
  • GEOS/3.9.1-GCC-11.2.0 GEOS (Geometry Engine

  • GMP/6.2.1-GCCcore-10.3.0 GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.

  • HH-suite/3.3.0-gompi-2021b easyconfig The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).
  • HMMER/3.3.2-gompi-2021a HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.
  • Kalign/3.3.2-GCCcore-11.2.0 easyconfig Kalign is a fast multiple sequence alignment program for biological sequences.

  • MPFR/4.1.0-GCCcore-11.2.0 The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.

  • MUMmer/4.0.0beta2-GCCcore-11.2.0 MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it.

  • MrBayes/3.2.7a-foss-2021b easyconfig MrBayes is a program for the Bayesian estimation of phylogeny.

  • Qhull/2020.2-GCCcore-11.2.0 Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull.

  • einops/0.7.0-GCCcore-12.3.0 Flexible and powerful tensor operations for readable and reliable code. Supports numpy, pytorch, tensorflow, jax, and others.