BOL

Brief Overview of Snakemake Pipeline Commands

The tabs below include a walkthrough of clustering 7 biological sequences (A-G) using the Unweighted Pair-Group Method with Arithmetic mean (UPGMA) method. Note that UPGMA is actually a generic method and thus the walkthrough could apply to any...

R phylogenetics is built on the contributed packages for phylogenetics in R, and there are many such packages. Let's begin today by installing a few critical packages, such as ape, phangorn, phytools, and geiger. To get the most recent CRAN version...

If you are on Conda, you can try installing cpamn  https://anaconda.org/bioconda/perl-app-cpanminus and then cpanm install <name>  

Here we walk through an end-to-end gene-level RNA-seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were quantified to the reference transcripts, and prepare gene-level count...

PaReBrick. The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as input data. It identifies rearrangements, tests them for consistency with a tree, and sorts the events by their...

We press the combination Alt keys+ F1 or Alt + F2, in the menu that opens, select NetBox, it is under the number 2. Now we need to create a connection to our server. Let's say you have data for connecting via SSH:Login: root, password: pass,...

You can also open an additional menu by holding down the button Shift, which is mainly intended for working with files and archives, namely: F1- add files to archive F2- extract files from archive F3- execute archive management...

Just F1 commands F1- show / hide the left panel F2- show / hide right panel F3- sort by file name F4- sort by extension F5- sort by recording time F6- sort by size F7- do not sort F8- sort by creation time F9- sort by access time F10-...

Alt, which is mainly intended for working with files and directories, namely: F1- open the current disk in the left pane F2- open the current disk in the right pane F3- here you can open the file for viewing both in an external program and in...

MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin)...

The #Uniclust90, #Uniclust50, #Uniclust30 databases cluster #UniProtKB sequences at the level of 90%, 50% and 30% pairwise sequence identity.

Latest blast software and old versions https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ 

Blast v2.12 wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.12.0+-x64-linux.tar.gz

Code Golf is a game designed to let you show off your code-fu by solving problems in the least number of characters. Since this is your first time here, I suggest starting with something simple like Fizz Buzz.

Blast database version 4 @ https://ftp.ncbi.nlm.nih.gov/blast/db/v4/

OrganellarGenomeDRAW converts annotations in the GenBank or EMBL/ENA format into graphical maps. The input has to be a GenBank or EMBL/ENA flat file wherase the output can vary among several types of files....