Do you HYPHY with (Data)Monkey !!
HyPhy, acronym for Hypothesis Testing Using Phylogenies (www.hyphy.org) was written & designed by Kosakovsky Pond and workers to provide likelihood-based analyses on molecular evolutionary data sets and help detect differential rates of variability within a coding sequence datasets. It is freely available, has a Graphical User Interface and can be used by anyone with or without much computer language or programming exposure.
It was earlier presumed that substitution rates were uniform over an alignment of homologous DNA/Protein sequences but many workers studying molecular evolutionary processes influencing rates and patterns of evolution negated this presumption with quite a lot of data and this is especially true for highly evolving gene family datasets and for viral genomes. Natural selection takes place at different domains/regions/sites which are under positive, negative or neutral selection pressures. Positive selection originates with more of non-synonymous substitutions in a protein coding sequence influencing the fitness advantage (protein structure and function) of an organism whereas negative selection takes place with more of synonymous substitution in a protein coding sequence leaving the amino acid sequence or protein structure and function unchanged. A neutral evolution is said to be taking place when the non-synonymous substitutions do not affect the protein structure and function and rate of non-synonymous substitutions. The rate of synonymous and non-synonymous substitutions is given by dS and dN respectively. In the case of neutral evolution, dS and dN are observed to be in equilibrium. Accordingly, the ratio of dN/dS given by ω=β/α (also referred to as dN/dS) has become a standard measure of selective pressure. The total ω for a sequence alignment is referred to as Global ω. Global ω with a value of approximately 1 signifies neutral evolution, below 1 suggests negative selection whereas ω more than 1 implies positive selection. To start with the analyses, all one needs is, a suitable codon substitution model as detected by MODELTEST program (available online), a nexus formatted sequence alignment file (must be codon data file) and a Maximum Likelihood tree of the data.
Datamonkey is a web interface (http://www.datamonkey.org) which uses HyPhy batch files to execute most of its tools and packages for the computational analyses. This web interface can be used for estimating dS and dN over an alignment of coding sequences and also for identifying codons and lineages under selection. It also provides “state of the art” tests of codon based models to infer signatures of positive Darwinian selection by comparing rates of synonymous (dS) versus non-synonymous (dN) mutations even in the presence of recombination. It actually reports ω (=dN/dS) using a variety of evolutionary models. Apart from this, Datamonkey also offers a number of packages such as GARD, SLAC, REL, FEL, EVOBLAST etc. These will be discussed in the next issue. Keep reading!!
A comprehensive list of references on the article are available upon request to the author ([email protected])
Installing Autodock4 on MacOS.
Previously, we installed the Autodock suite  on Ubuntu. Visit this article for details. Now, let’s install it on MacOS.
How to install Autodock4 on Ubuntu?
Autodock suite is used for docking small molecules . Recently, Autodock-GPU  is developed to accelerate the docking process. Its installation is described in this article. In this tutorial, we will install Autodock 4.2.6 on Ubuntu.
DS Visualizer: Uses & Applications
Discovery Studio (DS) Visualizer (from BIOVIA) is a visualization tool for viewing, sharing, and analyzing proteins . Here are some uses and applications of DS Visualizer.
Protein structure & folding information exploited from remote homologs.
Remote homologs are similar protein structures that share similar functions, but there is no easily detectable sequence similarity in them. A new study has revealed that the protein folding information can be exploited from remote homologous structures. A new tool is developed to recognize such proteins and predict their structure and folding pathway. (more…)
Pathonoia- A new tool to detect pathogens in RNA-seq data.
Detecting viruses and bacteria in RNA-seq data with less false positive rate is a difficult task. A new tool is introduced to detect pathogens in RNA-seq data with high precision and recall known as Pathonoia .
AlphaFill- New algorithm to fill ligands in AlphaFold models.
AlphaFold is a popular artificial intelligence based protein prediction tool . Though it predicts good protein structures, it lacks the capability to predict the small molecules present in the structure such as ligands. For this purpose, AlphaFill is introduced by Hekkelman et al.,. (more…)
How to calculate binding pocket volume using PyVol plugin in PyMol?
Previously, we provided a tutorial for PyVol plugin  installation. In this article, we will calculate the binding pocket volume of protein using the same plugin in PyMol . (more…)
How to generate electron density map using Pymol?
Electron density maps are available for most of the protein structures in PDB. Therefore, in this article, we are using PDB to generate electron density maps in Pymol.
Installing PyVOL plugin in Pymol on Ubuntu (Linux).
PyVOL  is an excellent plugin of Pymol  for pocket visualization of proteins. In this article, we will install the PyVOL plugin in Pymol on Ubuntu. (more…)
Tips & Tricks
How to download FASTA sequences from PDB for multiple structures?
In this article, we are going to download FASTA sequences for multiple structures from PDB . We need to have PDB IDs only for input. (more…)
How to install Kpax on Ubuntu (Linux)?
Kpax is a bioinformatics program to search and align protein structures . It is currently available for Linux platforms only. In this article, we are going to install the latest version of Kpax (5.1.3) on Ubuntu (Linux). (more…)
How to run do_dssp command (mkdssp) in Gromacs 2022?
In the latest version of GROMACS (2022) , there are some issues regarding the gmx do_dssp command. Apparently, this command either does not run displaying a fatal error, or if it runs then it does not read any frame from MD simulation files. In this article, we are going to run the same command for GROMACS 2022. (more…)
Installing SMINA on Ubuntu (Linux).
SMINA is a fork of AutoDock Vina supporting better scoring function and high-performance energy minimization . In this article, we are going to install SMINA on Ubuntu (Linux). (more…)
How to install ClusCo on Ubuntu (Linux)?
ClusCo is a bioinformatics software to perform clustering and comparison of protein models . In this article, we are going to install ClusCo on Ubuntu (Linux). (more…)
How to run LigAlign plugin on Pymol?
Running a plugin on an old version of Pymol  can give you multiple errors that are not easy to troubleshoot. For example, LigAlign plugin  runs on an old version of Pymol. Previously, we explained how to install LigAlign on Pymol. In this article, we will run the LigAlign command on Pymol. (more…)
How to install the LigAlign plugin on Pymol on Ubuntu (Linux)?
Few errors appear when we try to run the LigAlign plugin  in Pymol . For example, if you try to run the ligand_alignment plugin, it will give you multiple errors including “Unable to initialize LigAlign v1.00“, or “can’t run LigAlign v1.00” or “incorrect Python syntax” or “Plugin has been installed but initialization failed“. In this article, we explain the reason for this issue and how you can rectify these errors. (more…)
How to install multiple Pymol versions on Ubuntu (Linux)?
Sometimes we need to access old versions of Pymol . Running some plugins on Pymol is difficult due to Python incompatibility. New Pymol versions require Python 3.x whereas older versions run on Python 2.x. Therefore, we need to maintain multiple versions of Pymol on a single system. In this article, we will install Pymol 1.7.x along with the latest version (Pymol 2.5.2) on Ubuntu. Later, we will create shortcuts for them.
[Tutorial] Installing Pymol on Mac OS.
Previously, we provided a tutorial for Pymol installation on Ubuntu. In this article, we are going to install Pymol on Mac OS. (more…)
How to install VMD on Ubuntu?
In this article, we are going to install VMD  on Ubuntu. (more…)
How to install GROMACS on Apple M1 (MacOS)?
We have provided a few articles on GROMACS installation on Ubuntu. In this article, we are going to install GROMACS  on Mac OS. (more…)
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