Comparing MacVector with Assembler with Sequencher

Sequencher does not run on macOS 10.15 ("Catalina")

If you use the popular Sequencher sequence assembly program from Genecodes you cannot run the current version of Sequencher

The root of this problem is that Sequencher 5.4.6 (the latest version for the Mac) is a 32-bit application and is particularly reliant on an ancient "Carbon" OS 9-compatibility framework that Apple has been telling developers for many years will be phased out in the near future. That day ihas finally arrived and until Sequencher is completely rewritten for the latest macOS, you cannot upgrade your Mac to Catalina..

MacVector with Assembler has been fully 64-bit for many years (since MacVector 13) and has no dependency on the "Carbon" framework. It provides almost all of the functionality of Sequencher within an updated modern interface, along with a host of additional functionality and integration with all of the DNA analysis tools within the core MacVector application.

For a limited time, we are offering a 50% discount to all Sequencher users who wish to upgrade to MacVector with Assembler. There are more details here.

Project Interface

Like Sequencher, MacVector with Assembler provides a simple Project-oriented interface where you can import and drag and drop files for Assembly. Unlike Sequencher, MacVector lets you have multiple projects open at one time.

Viewing and Editing Contigs

Sequencher uses two coordinated windows to displaythe contig alignment and any associated chromatogram files;

MacVector displays the information in two panes in a single window, along with (optionally) quality information. Unlike Sequencher, trimmed bases are not deleted, but are simply shown greyed out and can be hidden/shown with a simple toolbar button click.. A unique "Dots" mode (not shown) replaces residues that match the consensus with a dot so that your eyes are immediately drawn to SNPs and other mismatches.

Comparison of MacVector with Assembler and Sequencher Functionality

While not every Sequencher function and feature is present in MacVector with Assembler and MacVector provides many additional sequence analysis functions that are not present in Sequencher, the two applications are broadly similar when it comes to de novo and reference-based assembly capabilities. The table below list the major features present in the two programs;

	MacVector with Assembler	Sequencher
Assembles ABI Data	Yes	Yes
Assembles NGS Data	Yes	Yes
Simple Project Interface	Yes	Yes
de novo Assembly	Phrap, Velvet, SPAdes, Flye	Sequencher, Velvet
Base calling with Quality Values	Phred	Sequencher
Reference Assembly	Bowtie, MacVector	Sequencher, BWA, GSNAP, Maq
Built-in Reference Assembly Editor/Viewer	Yes	Requires external Tablet viewer
Supports Quality Values	Yes (standard phred values)	Yes (Sequencher)
SNP Detection	Yes	Yes
Multiple Sequence Alignment	ClustalW, MUSCLE, T-Coffee	ClustalW, MUSCLE
Restriction Enzyme mapping	Extensive	Minimal
Variant calling with SAMtools	Yes	Yes
Multiplex ID	No	Yes
Modern graphical interface	Yes	No
High quality vector-based graphical export	Yes	No
64-bit	Yes	No
Compatible with future macOS releases	Yes	No
Scan fasta/q files and retrieve matches	Yes	No
Built-in NCBI BLAST	Yes	No
Extensive DNA analysis and editing tools	Yes	No
Save unaligned reads to separate file(s)	Yes	No