In pmgrollemund/phyloHIV:

options(width = 100)
knitr::opts_chunk$set(echo = TRUE, dev = c('png','pdf'), fig.width= 12, 
                      fig.height=8,
                      collapse = TRUE,
                      comment = "#>"
)

Purpose of the document

In this document, we describe how to run an example from genomic sequences to transmission chains. The example input are in the package folder.

For what follows, you should open a terminal session and change the directory to the package folder.

Blast and align the sequences

Run the following terminal command: ```{bash, echo = TRUE,eval=FALSE} cd inst Rscript extscript/align_sequences.R extjson/options.json

### Build the trees
Run the following terminal command: 
```{bash, echo = TRUE,eval=FALSE}
Rscript extscript/build_trees.R extjson/options.json

Ancestral state reconstruction and extract subtrees

Run the following terminal command: {bash, echo = TRUE,eval=FALSE} Rscript extscript/Ancestral_state_to_clades.R extjson/options.json

pmgrollemund/phyloHIV documentation built on Nov. 5, 2019, 12:56 a.m.