README.md

In Takheer/NWPA: Needleman-Wunsch pairwise alignment

NWPA

Implementation of Needleman-Wunsch pairwise alignment of DNA sequences in R language. It supports sequences with ambigious base counts and gapped sequences. Moreover, this library provides two function to read and write FASTA files.

Installation:

devtools::install_github("Takheer/NWPA")

Usage of align:

align("example_1.fas", "alignedSequences.fas")

Will align two first sequences from example_1.fas file and will write them aligned into alignedSequences.fas Default settings are 1 for match, 0 for mismatch and -1 for gap insertion/deletion

You can also set your own values:

align("example_1.fas", "alignedSequences.fas", match=0, mismatch=-2, gap=-1)

Takheer/NWPA documentation built on May 15, 2019, 3:24 p.m.