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.

A R version supports more than one version of Bioconductor. To take advantange of new features, users have to update Bioconductor packages regularly.

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.

The Tab-Separeted Values (TSV) file is a simple text format and widely supported. The data are stored in a tabular structure, each record in the table is one line of the text file. And each field value of a record is separated by a tab character.

It is easy to operate TSV files in programming languages. But if the file were quite large, for instance, millions of lines, it would be difficult to operate the file. Under this circumstances, load the large TSV file into an SQLite3 databasea would be convenient for further operations.

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.

Jellyfin is a Free Software Media System that puts you in control of managing and streaming your media. It is an alternative to the proprietary Emby and Plex, to provide media from a dedicated server to end-user devices via multiple apps.

Here recorded the walkthrough of install and setup of Jellyfin docker image in a Debian bullseye/11.2 x86-64 NAS.

There is still no official OneDrive client for Linux, the project “OneDrive Client for Linux” is the only choice. It provides a powerful and highly configurable client can run on all major Linux distributions, FreeBSD, or as a Docker container. It supports one-way and two-way sync capabilities and securely connects to Microsoft OneDrive services.

This post is the workthrough of installation and configuration of OneDrive Linux ina headless Debian bullseye/11 server.

MetaPhlAn (Metagenomic Phylogenetic Analysis) is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.

This post describes the installation and setup of MetaPhlAn 3.0 in Debian 11/bullseye.

Last updated at: 2021-12-17.

Here are some miscellaneous tips for working on RStudio and writing R Markdown file. This blog will be updated from time to time.

See also:

• RStudio Cheatsheets