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{r setup, include=FALSE} # knitr header - do not touch knitr::opts_chunk$set(echo = TRUE)

install.packages(“BiocManager”) library(BiocManager)

install.packages(“devtools”) library(“devtools”)

Github

install.packages(“compbio4all”) library(“compbio4all”) install(“compbio4all”)

Bioconductor

install.packages(“Biostrings”) install(“Biostrings”) library(“Biostrings”)

install.packages(“ggmsa”) library(ggmsa)

install(“ggmsa”) library(“ggmsa”)

install(“msa”) library(“msa”)

CRAN

install.packages(“rentrez”) library(rentrez)

install.packages(“seqinr”) library(seqinr)

install.packages(“ape”) library(“ape”)

R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.

When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

{r cars} summary(cars)

Including Plots

You can also embed plots, for example:

{r pressure, echo=FALSE} plot(pressure)

Note that the echo = FALSE parameter was added to the code chunk to prevent printing of the R code that generated the plot.