Seqotron: a user-friendly sequence editor for Mac OS X.

Mathieu Fourment,Edward C Holmes

doi:10.1186/s13104-016-1927-4

Abstract

BackgroundAccurate multiple sequence alignment is central to bioinformatics and molecular evolutionary analyses. Although sophisticated sequence alignment programs are available, manual adjustments are often required to improve alignment quality. Unfortunately, few programs offer a simple and intuitive way to edit sequence alignments.ResultsWe present Seqotron, a sequence editor that reads and writes files in a wide variety of sequence formats. Sequences can be easily aligned and manually edited using the mouse and keyboard. The program also allows the user to estimate both phylogenetic trees and distance matrices.ConclusionsSeqotron will benefit researchers who need to manipulate and align complex sequence data. Seqotron is a Mac OS X compatible open source project and is available from Github https://github.com/4ment/seqotron/.

Highlights

Accurate multiple sequence alignment is central to bioinformatics and molecular evolutionary analyses
There are a large number of sequence editors that allow sequence alignments to be displayed, including Se-Al [3], Jalview [4], SeaView [5], Mesquite [6] and UGENE [7]
One or a group of sequences can be manually edited by dragging regions of the alignment using the mouse in a similar way to Se-Al

Summary

Introduction

Accurate multiple sequence alignment is central to bioinformatics and molecular evolutionary analyses. Sophisticated sequence alignment programs are available, manual adjustments are often required to improve alignment quality. Few programs offer a simple and intuitive way to edit sequence alignments. State-of-the-art methods of multiple sequence alignment such as MUSCLE [1] and MAFFT [2] are usually used to automatically generate alignments. These methods can be inaccurate when the input sequences are highly dissimilar or when sequencing errors have been incorporated. Only a few (e.g. Se-Al) provide a simple and intuitive way to edit sequence alignments. It is often problematic to convert files into different file formats, even though a wide variety of formats are required for different applications

Objectives

Results

Conclusion