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Sequence Analysis Tools for Molecular Biologists

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Multiple Sequence Alignment

You can use MacVector to align related DNA or Protein sequences. MacVector uses the ClustalW algorithm to automatically align any number of sequences and provides a sophisticated editor that lets you fine tune the alignments. The alignments can be output in a variety of formats or used to generate phylogenetic reconstructions using a number of built-in algorithms.

Creating Alignments

You can create alignments from sequence already open in MacVector, or by creating an empty alignment and populating it with sequences imported from disk. You can also directly open an existing file containing multiple sequences. MacVector supports the following multiple sequence file formats:

MacVector

PHYLIP

NEXUS

FastA

GCG MSF

GCG RSF

You work with alignments in the multiple sequence alignment editor. Sequences can be viewed using plain monochrome text or colored according to user-defined color groups.

MultSeqAFig1

Residues can be colored according

Automatic Alignments

MacVector uses the ClustalW algorithm

MultSeqAFig2

As well as exposing all

Editing

The MSA editor provides full

MultSeqAFig3

This dialog provides fine control

There are a variety of parameters and modes that control how the residues appear on-screen. For example, you can set up the editor so that all matches to the consensus are displayed as dots - this is very useful for identifying variant regions in otherwise closely related sequences.

MultSeqAFig4

Variant regions in closely related

Output Options

The aligned sequences can be displayed in result windows in a variety of different ways. One window provides a high quality customisable graphical text display designed for output on a laser printer, while another duplicates the output from ClustalW. You can also view the sequences aligned in pairwise mode, along with a matrix displaying the identities and similarities of each pair of sequences.

MultSeqAFig5

The pairwise similarity matrix window

MultSeqAFig6

The customizable alignment picture display

Phylogenetic Reconstruction

You can use MacVector to

The reconstructed phylogeny is viewed

MultSeqAFig7

A dendrogram produced by phylogenetic

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Overview

Comparison of MacVector Editions

MacVector Cloning Edition

What has changed since my version?

What's New in MacVector?

Graphical Sequence Editing

Agarose Gel Simulation

Gateway and TOPO Cloning

Gibson/LIC Assembly

Auto-annotation

Primer Design

DNA Analysis

Protein Analysis

Database Searching

Multiple Sequence Alignment

Sequence Confirmation

cDNA Alignment

macOS Mojave Dark Mode

System Requirements

Screencasts