Apr 19 2024
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cryoCARE
PIP package memory efficient implementation of cryoCARE (Content-Aware Image Restoration for Cryo-Transmission Electron Microscopy Data), is a restoration method that dramatically increases contrast in cryo-TEM images, improving the interpretability of the acquired data.
Updated versions:
0.3.0 | Linux 64
0.3.0 | OS X INTEL
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Apr 18 2024
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BCFtools
a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
Updated versions:
1.20 | Linux 64
1.20 | OS X INTEL
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Apr 17 2024
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breseq
a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for microbial sized genomes. It reports single-nucleotide mutations, point insertions and deletions, large deletions, and new junctions supported by mosaic reads.
Updated versions:
0.38.3 | Linux 64
0.38.3 | OS X INTEL
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Apr 17 2024
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DeepChem
Updated versions:
2.8.0 | Linux 64
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Apr 17 2024
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NGLView
is an IPython/Jupyter widget to interactively view molecular structures and trajectories.
Updated versions:
3.1.2 | Linux 64
3.1.2 | OS X INTEL
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Apr 16 2024
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cryoDRGN
a neural network based algorithm for heterogeneous cryo-EM reconstruction. In particular, the method models a continuous distribution over 3D structures by using a neural network based representation for the volume.
Updated versions:
3.2.0-beta | Linux 64
3.0.1-beta | Linux 64
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Apr 16 2024
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Eternafold
performs RNA secondary structure prediction.
Updated versions:
1.3.1 | Linux 64
1.3.1 | OS X INTEL
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Apr 16 2024
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doubleHelix
is a tool for nucleic acid sequence identification, assignment and validation tool for cryo-EM and crystal structure models.
Updated versions:
20240312 | Linux 64
20240312 | OS X INTEL
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Apr 16 2024
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CheckMySequence
is a sequence assignment validation tool for in cryo-EM models
Updated versions:
20240312 | Linux 64
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Apr 16 2024
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EMRNA
is a deep learning based automated RNA modeling from cryo-EM maps.
Updated versions:
1.4 | Linux 64
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Apr 16 2024
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spIsoNet
Single Particle spIsoNet (spIsoNet) is designed to correct for the preferred orientation problem in cryoEM by self-supervised deep learning, by recovering missing information from well-sampled orientations in Fourier space.
Updated versions:
1.0_cu11.8 | Linux 64
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Apr 16 2024
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SAMtools
(Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.
Updated versions:
1.20 | Linux 64
1.20 | OS X INTEL
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Apr 15 2024
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IMP
(Integrative Modeling Platform) designed to allow mixing and matching of existing modeling components as well as the easy addition of new functionality.
Updated versions:
2.14.0 | OS X INTEL
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Apr 15 2024
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subTOM
(Subtomogram averaging scripts with TOM toolbox or Subvolume processing scripts with the TOM toolbox) is a collection of scripts for a pipeline for subvolume alignment and averaging of electron cryo-tomography data.
Updated versions:
1.1.6 | Linux 64
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Apr 15 2024
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PHENIX
(Python-based Hierarchical Environment for INtegrated Xtallography) a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.
Updated versions:
1.21.1-5286 | Linux 64
1.21.1-5286 | OS X INTEL
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Apr 14 2024
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IMP
(Integrative Modeling Platform) designed to allow mixing and matching of existing modeling components as well as the easy addition of new functionality.
Updated versions:
2.20.1 | OS X INTEL
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Apr 12 2024
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Dynamo2Relion
Convert Dynamo Tables to Star Files for RELION 4.0
Updated versions:
1.0.0 | OS X INTEL
1.0.0 | Linux 64
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Apr 11 2024
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LightDock
a protein-protein, protein-peptide and protein-DNA docking framework based on the Glowworm Swarm Optimization (GSO) algorithm.
Updated versions:
0.9.4 | Linux 64
0.9.0 | Linux 64
0.9.4 | OS X INTEL
0.9.0 | OS X INTEL
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Apr 11 2024
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evo
DNA foundation modeling from molecular to genome scale
Updated versions:
0.1.1 | Linux 64
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Apr 09 2024
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Spring
(Single Particle Reconstruction from Images of kNown Geometry) a single-particle based helical reconstruction package for electron cryo-micrographs used to determine 3D structures of either highly ordered or less ordered specimens.
Updated versions:
0.86.1661 | OS X INTEL
0.86.1661 | Linux 64
0.87.1723 | Linux 64
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Apr 08 2024
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TomoNet
a software package with a modern graphical user interface to carry out the entire pipeline of cryoET and subtomogram averaging to achieve high resolution.
Updated versions:
beta_03 | Linux 64
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Apr 07 2024
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Ghostscript
an interpreter for the PostScript (TM) language. It can display and convert postscript files. Software can be involved with gs command.
Updated versions:
10.03.0 | Linux 64
10.03.0 | OS X INTEL
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Apr 05 2024
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cs2star
A simple utility that wraps around csparc2star.py to convert particle positions from Cryosparc JOB directories into a RELION-ready directory.
Updated versions:
0.6.6 | OS X INTEL
0.6.6 | Linux 64
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Apr 04 2024
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Foldseek
enables fast and sensitive comparisons of large structure sets.
Updated versions:
8-ef4e960 | Linux 64
8-ef4e960 | OS X INTEL
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Apr 02 2024
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Infernal
(INFERence of RNA ALignment) searches DNA sequence databases for RNA structure and sequence similarities and uses a special case of profile stochastic context-free grammars called covariance models (CMs). In many cases It is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.
Updated versions:
1.1.5 | Linux 64
1.1.5_arm | OS X INTEL
1.1.5 | OS X INTEL
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