Software

• Kindly provided by Xu Meng.

This post descripts the way to install R and Rstudio in Windows using Scoop.

While using ZDOCK in Debian 11, an error message shew:

$ ./mark_sur
./mark_sur: error while loading shared libraries: libg2c.so.0: cannot open shared object file: No such file or directory

Severe acute respiratory syndrome coronavirus 2 Wuhan-Hu-1 (NC_045512.2) and hCoV-19/Wuhan/WIV04/2019 (EPI_ISL_402124) are two general used reference genome sequences used for SARS-CoV-2 phylogenetic analyses.

Here is the alignment result of these two sequences by EMBOSS needle.

There are nearly 14 million viral genome sequences right now in the GISAID EpiCoV ™ database. It is not likely to infer the phylogenetic relationships for such a huge dataset by traditional maximum likelyhood or Bayesian methods in a shor time period. The UShER package was developed to generate ultra-large phylogenetic tree of SARS-CoV-2 genomes. The algorithm of the UShER program is to place new samples onto an existing phylogeny using maximum parsimony method. It is able to place given SARS-CoV-2 genome sequences into the GISAID global phylogeny in a couple of hours. This program is particularly helpful in understanding the relationships of newly sequenced SARS-CoV-2 genomes with each other and with previously sequenced genomes in a global phylogeny.

The UShER package is composed by four programs:

1. UShER: a program that rapidly places new samples onto an existing phylogeny using maximum parsimony.
2. matUtils: a toolkit for querying, interpreting and manipulating the mutation-annotated trees (MATs).
3. matOptimize: a program to rapidly and effectively optimize a mutation-annotated tree (MAT) for parsimony using subtree pruning and regrafting (SPR) moves within a user-defined radius.
4. RIPPLES: a program that uses a phylogenomic technique to rapidly and sensitively detect recombinant nodes and their ancestors in a mutation-annotated tree (MAT).

The taxoniumtools and Taxonium website are used to display the MAT generated by UShER.

yt-dlp is a youtube-dl fork and able to download videos and audios from many streaming platforms, such as YouTube.

This blog describes installation in Debian bullseye and some common usage examples.

MrBayes 3 is a program for Bayesian inference and model choice across a large space of phylogenetic and evolutionary models. And BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. BEAGLE is able to accelerate MrBayes analyses very much.

This post introduces the way to run MrBayes along with BEAGLE.

Due to the limited space of EndNote online, I still used to sync EndNote libraries through OneNote. The drawback is, the library might be corrupted occasionally (about once a couple of months).

I have introduced how to install R and RStudio Server before. But free version of RStudio Server lack of many security features, especially SSL.

This post introduces to secure RStudio Server by an Nginx reverse proxy.

This post was first released at 2019-05-26, and updated at 2021-04-20.

Since PyMOL 2.x released, there were no binary installer avaliable for Windows.

PyMOL Wiki provides the way to install open source PyMOL in Windows under Python 3.x.

This post provided the method to install PyMOL 2.x by conda (Anaconda or Minoconda) in Windows.

BEAGLE is a high-performance library to accelerate the calculations of Bayesian and Maximun Likelihood phylogenetics analyses. The latest version of beagle-lib was released on Dec 4, 2018.

When compiled for NVidia Tesla V100 on Debian buster 10.9, an error was encountered:

nvcc fatal   : Value 'compute_30' is not defined for option 'gpu-architecture'