seqUtils/README.Rmd at master · SamT123/seqUtils · GitHub

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---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# seqUtils

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Tools for working with biological sequences in R.

## Overview

`seqUtils` provides tools for common sequence analysis
tasks (read & write FASTA files, translate/align/compare sequences, etc.).

## Installation

You can install the development version of seqUtils from
[GitHub](https://github.com/) with:

```r
# install.packages("devtools")
devtools::install_github("SamT123/seqUtils")
```

## Requirements

- MAFFT (for alignment)
- cmaple (for tree building)

## Example

```{r example, eval=FALSE}
library(seqUtils)

# Read FASTA file
sequences <- fast_fasta("sequences.fasta")

# Translate to amino acids
aa_sequences <- translate(sequences)

# Find substitutions compared to a reference
substitutions <- get_substitutions(
  reference_seq,
  query_seqs,
  exclude = c("X", "N")
)
```