I$\text{'}$m having some trouble executing the codes and getting results on windows. Some screenshots of the results would be appreciated

About the data You will use whole genome data from SARS and Covid$-19$ at the National Center for

Biotechnology Information $($NCBI$)$ RefSeq genome collection. Specifically, you will download the coding

sequence $($CDS$)$ data for each genome using biomartr package in R$.$

Approach You will use biomartr packge to download the CDS sequences for SARS and Covid$-19.$ You

will then use the orthologr R package to identify orthologs using reciprocal best hit $($RBH$)$ approach, align

with Clustal Omega $($clustalo$),$ run pal$2$nal to convert protein alignments back to nucleotide alignments, and

finally estimate dN$,$ dS and dN$/$dS from multiple sequence alignments. This can all be done with $3$ simple

commands executed in RStudio.

Configuring your computer for orthologr It is anticipated that configuring your computer could take

some time depending on your OS and personal computer configuration. Your instructor will dedicate a

session to working with students and answering questons. If you are not familiar with software compilation

and installation, then this is an excellent opportunity to learn more.

You will need to configure your computer with two software: Blast$+$ and KaKs$\_$Calculator $($version $1\mathrm{.}2).$

This is relatively straightforward for MacOS and Linux operating systems, but could be more challenging

for Windows users.

Instructions provided below are only for Linux$/$MacOS users. It should be possible complete the

project on Windows operating system with WSL or some other linux emulator. However, for WSL we have

encountered difficulties compiling Ka$\_$Ks$\_$Calculator from source in the past. Please reach out to your

instructor if you are using WSL and encounter difficulties.

Some basic instructions for configuring your computer for orthologr at the drostlab github

Note that you can skip all software except the three mentioned above.

Blast$+$ should have pre$-$compiled executables available for your operating system. In other words, you do

not need to compile these softwares from source.

KaKs$\_$Calculator can be downloaded from here and must be compiled from source: google kaks$\_$calculator

Please download version $1\mathrm{.}2$ with description $$KaKs$\_$Calculator

$1$

Version $1\mathrm{.}2-$ Command Line for Linux$/$Mac$.$ Instructions for how to install can be found at the drostlab

github page listed above.

Your instructor recommends placing all binaries $($executable files$)$ in your $/$usr$/$local$/$bin directory. This

is the standard location for third$-$party softwares on Unix$/$Linux$-$based operating systems and will help

you avoid issues when running orthologr. For Blast$+,$ you only need to copy makeblastdb and blastp

executables to $/$usr$/$local$/$bin $($the others are not necessary for your assignment$).$

Install $$orthologr$.$ See instructions at the drostlab github page above.

Install $$biomartr$.$ See instructions at biomartr github

Tasks The commands you need to execute are listed at the drostlab github page in the section $$Example:

Computing dN$/$dS values for all orthologous genes between two genomes$$: google github drostlab orthologr #example$-$computing$-$dnds$-$values$-$for$-$all$-$orthologous$-$genes$-$between$-$two$-$genomes

Instead of comparing whole mouse and human genes, we will instead compare SARS and Covid$-19$ and need

to modify the code for this purpose.

Please modify the biomart::getCDS commands to download organism $$GCF$\_009858895\mathrm{.}2$ for Covid$-19$

and $$GCF$\_000864885\mathrm{.}1$ for SARS and define sensible variable names.

After running the biomart code, it is common to see the error $$The download session seems to have timed

out at the FTP site $...$ This can appear even when the files downloaded correctly. To be sure, you can

always compare the md$5$ hash using the md$5$sum $($Linux$)$ or md$5($MacOs$)$ commands from your terminal

and confirm the hashes match those in the downloaded file $*$md$5$checksums.txt$$ which contains the hashes

of the files on the NCBI ftp site.

Modify the dNdS command query$\_$file argument to specify the Covid$-19$ cds file from the biomart::getCDS

step.

Modify the dNdS command subject$\_$file argument to specify the SARS cds file.

You can use the pairwise alignment approach with $$NW$($Needleman$-$Wunsch$)$ algorithm, otherwise you

will need to install additional standalone alignment software. This Needleman$-$Wunsch approach produces

very similar results as aligning with Clustal Omega and is fine for this assignment.

When you you are ready, you can run the code.