Testimonials
"Sequencher, from Gene Codes of Ann Arbor, Mich., is possibly today's most popular software for DNA Sequencing."
Steven D. Buckingham
Sequence Analysis Software Update
The Scientist
December 20, 2004
"Sequencher 4.10.1 contains a welcome new feature that keeps track of protein and cDNA numbering in DNA assemblies. This ability greatly simplifies the task of comparing your experimental data to a genomic DNA reference when looking for mutations or other changes. This feature alone reinforces Sequencher as one of the premier tools for sequence analysis."
David Adams M.D Ph.D
Clinical Investigator and Sequencher 4.10.1 beta tester
"I am very satisfied with how sequencher handles heterozygous calls in autosomal sequencing and potential heteroplasmies in mitochondrial resequencing. I found the forensics addon package for the general foresnsics community to be very helpful!"
Eric Wang, Ph.D
Statistical Geneticist, Algorithm Development and Data Analysis
Affymetrix, Inc.
"I have been involved in DNA sequencing projects since I got my masters degree in bioinformatics in 2002. The programs I used for sequences analysis included Vector NTI from Invitrogen, PhredPhrap, Lasergene from DNAStar, and Sequencher. Sequencher is my favorite program not only because of its powerful SNP analysis functions but also because it is very easy to use and user friendly. I would like to recommend Sequencher to people who are doing SNP research projects and/or responsible for training students and colleagues who are going to do genotyping work."
Zongying Xi, MD/MS
Department of Pharmaceutical Sciences
St Jude Children's Research Hospital
"After using Sequencher for years as a grad student, I was forced to switch to MacVector as a postdoc in a new lab. Sequencher is so much easier to use than MacVector and has such a superior interface that I used the demo version of Sequencher for months rather than the lab copy of MacVector. Sequencher feels as though it is written by biologists that can write software, rather than programmers attempting to write biological software. Any life scientist who has spent time pulling their hair out over non-intuitive software will greatly appreciate this distinction."
Dave Parker
University Of Michigan
Cell And Developmental Biology
"I am involved in resequencing projects for disease association studies. Sequencher was of tremendous help to me in these projects for- discovery of SNPs, detection of known SNPs, intronic/exonic SNPs & amino acid changing SNPs. I have been using it for sequence analysis of ABI data files since 2000. It is easy to operate and user friendly. It was a pleasure to be involved in the beta test program for version 4.6. What I liked in this new version is assembly function & variance table. Assemble to reference by defining assembly parameters using advance expression feature is very useful, it saves a lot of time and sequences can be assembled by defining feature of your choice e.g. sample ID, primer ID, or well position etc. Technical Support group at the Gene Codes Corporation has been very receptive to the idea of introducing variance table. With this feature it is now possible to export genotypes. Using this feature I am not only able to export whole table but also selected few columns using “export selected” option button."
Manjula Maheshwari
Human Genome Sequencing Center
Baylor College of Medicine
Houston, Texas
"Thank you for sending the demo version of Sequencher. This seems to be wonderful software for phylogenetic and mutation studies. It clearly indicates start and stop codons in DNA sequences. Sequencher is easy to use and allowed us to quickly align sequences from various individuals. This software is very user friendly, and the instruction manual is very informative. The contig assembly tool is quite amazing in its speedy and time saving functions, which are the requirements for researchers in the biochemical field. I really got exited by running this software."
Dr V.R.C. Murty
Department of Chemical Engineering
Manipal Institute of Technology
"The most popular request I receive in the in the DNA core lab is: find the good clone among this group of 'candidate' minipreps. Alignment of ABI data files against a 'reference' sequence (template file) quickly eliminates defectives by showing not only base changes but the consequences to the protein translation.
"The second most popular request is: validate this new maxiprep so it can be given to ... or used for ... or expressed in ... Rapid assembly and editing of total plasmid sequence and then comparison to the reference file on record is all done in Sequencher.
"The third most popular request is: compare this library of (protein improvement) mutants and tell me which ones have protein changes. This is done by alignment in Sequencher and then formatting the Summary view to display the resulting changes in protein translation.
"For my own projects, I use Sequencher as a very general multiple-alignment sequence editor. Most recently, I've been using it to make comparisons of genes retrieved from the databases for cross-species cDNA cloning. Showing regions of homology at the protein level and then having the colinear DNA sequence presented in the same view (Summary window) helps find regions suitable for primer design. Turning on the 'Matching Bases/Residues as Dashes' quickly shows regions of homology and divergence. I design primers to either or both depending on the project."
Dean Regier
Research Scientist
DNA core laboratories
"We have been using Sequencher in recent months in our Lab. Primarily, we perform aligning patient sequences from quite a lot of different genes and then check for polymorphisms and mutations. Our sequences are generated using the MegaBace capillary sequencing device.
"What we like so much about this fine piece of software is its very good structure and compact design, which also offers a great deal of flexibility. Sequencher lets you generate complex aligning projects within minutes and delivers constantly reliable results independent from the format in which your sequences were generated. And it computes with striking speed. Even staff with less experience in handling computers and software were able to use Sequencher autonomously without problems in an impressively short amount of time. What I like very much about Sequencher is that you do not drown in overloaded menus. Everything you need is very well and organized in a sophisticated way. This allows us to set up, customize, and edit our projects on the fly.
"This piece of software was developed by using three essential principles that occupy a central position in modern and successful science: knowledge, brain-sharing and communication. The same is true for the support Gene Codes offers for their product."
Boris Leuenberger
University of Hamburg
Laboratory of Molecular Genetics
"Sequencher is a fantastic application. It is easy to use and has facilitated the analysis of sequence data from a range of projects in our lab. We have been running the Mac OS X version on a dual processor Power Mac G5 and have used the program to process and assemble a large collection of ESTs that we have generated.
"Gene Codes also provides outstanding technical support, which has helped us take advantage of many advanced features of the program. I highly recommend Sequencher because it provides powerful sequence-analysis tools in an easy-to-learn interface".
Ricardo M. Zayas, PhD
Department of Cell & Structural Biology
University of Illinois at Urbana-Champaign
"Sequencher has been invaluable in our studies of the developmental changes in cardiac energy metabolism. We have used Sequencher in identification and cloning of several cardiac-specific genes critical to the energy-producing reactions in the fetal and newborn heart."
Tom Scholz
University of Iowa
"I have used Sequencher for regular sequence editing, for insilico cloning of plasmid constructs (such as reporter constructs) AND for contig management and assembly as part of whole genome sequencing projects."
Martin G. Klotz, PhD
Associate Professor
Department of Biology
University of Louisville
"We have been using Sequencher since 2001, and we are particularly impressed with its incorporation of powerful and time-saving features (such as alignments to reference strands and confidence-value trimming) into an easy-to-use, accessible package. Sequencher is our first choice for sequence analysis and editing.
"Though I frequently hear about other software packages that promise new features and improved sequence analysis, I find that Sequencher consistently offers the best combination of power and usability for our research group."
David O'Connor
Regional Primate Research Center
University of Wisconsin
"We've been satisfied Sequencher users for many years. In its current Mac OS X native form, it provides a powerful, user-friendly, and visually appealing tool for generating finished sequence products from raw ABI3730 data files. Recent enhancements, such as color-coded base confidences and single-key (spacebar) navigation, have improved our editing productivity significantly."
Richard Tizard
Principal Scientist
Discovery Biology
Biogen Idec, Inc.
"I have been using Sequencher for over 10 years, in three different labs, on both Macs and PCs. I simply could not get my sequence analysis done in such a timely manner without it! It's user-friendly, it's intuitive, and it's basically part of my brain now. Gene Codes is very responsive to their users' requests for improvements in their updates. I've tested similar programs over the years, and I keep coming back to Sequencher,because, YES, it is that good."
Lisa Clepper
Oregon Health Sciences University
"Sequencher's ease of use has allowed us to quickly align sequences from different individuals, resulting in the discovery of several new SNPs among our candidate disease genes. In addition, while most molecular biology laboratories could not function today without an oligonucleotide master catalogue, we have found Sequencher to be indispensable to help us construct a map catalogue, allowing us to easily visualize the locations of our PCR primers and gene probes."
David M. Iovannisci, MS, PhD
Birth Defects Research Lab
Children's Hospital and Research Center at Oakland
"I've been using Sequencher to assemble two complete organellar genomes, a chloroplast genome (105kbp) and a mitochondrial genome (40 kbp). In addition, Sequencher has been used in the lab to cluster cDNA sequences from an EST project, and for general sequence management. We handle several thousand sequences each year.
"I have found Sequencher to be very user-friendly. Some of the tools that were most useful for me were the contig assembly, the ability to translate to amino acid sequence in the three possible frames for each strand, and the overview mode, in which start and stop codons are shown clearly. The contig assembly tool is particularly good. It is easy to set the parameters, and it is also possible to assemble two sequences manually, mindlessly end to end. Furthermore, sequences can be selected by several different characteristics, such as the sequence name, chromatogram, etc.
"The ease of adding features to the sequences and being able to edit them later was another big advantage of using Sequencher."
Maria Virginia Sanchez Puerta
Cell Biology and Molecular Genetics
University of Maryland, College Park
"Many of my colleagues skip sequencing analysis and just put their sequences straight into Sequencher. It is intuitive to use. Our summer students pick up on it with a minimal amount of mentoring. Unlike ABI, Gene Codes still supports Macs, which makes our lives easier. Thank you!"
Rita Svensson
Los Alamos National Laboratories
"Sequencher is a great product. It allows you to easily analyze your data, looking directly at the chromatograms, trimming off the bad sequences as you import so that everything aligns easily, usually the first time. The large gap feature makes it easy to compare cDNA to genomic sequences. And the absolute best part of Sequencher is that Gene Codes is responsive to changes that help the researcher and is always listening to customer feedback. The tech support is also very good. They're always available to help with any questions."
Roxann Ashworth
Institute of Genetic Medicine
Johns Hopkins University
"Sequencher, for us, has proven very effective at facilitating the analysis of many genes, and in our ultimate goal of mutation discovery. Its functionality permits quick distillation of large amounts of raw data into manageable collections of sequences that are easily screened for variation. Built in to many of the program's time-saving features are user-specified adjustments that enable each analyst to define a customized comfort or confidence level based on a project's previous performance and expectations. While mutations can be detected in many ways, sequence analysis continues to be the gold standard, so I expect that Sequencher will continue to be an invaluable tool for us."
Mark Kimak
Department of Human Genetics
University of Pittsburgh
"We have been using Sequencher in our lab for over two years and can't imagine life without it! Before we purchased Sequencher, we tried several free-ware programs, and not one was as user friendly or had as many great features as we have found in Sequencher. Data analysis is a critical step in the experimental procedure, and this process is made so much easier when you have software as quick, efficient and thorough as Sequencher."
Liesel FitzGerald PhD Candidate
Menzies Research Institute
Tasmania, Australia
"Thanks for hearing me out on this and many other features of Sequencher. I've enjoyed using it for many of my projects, and it is by far one of the easiest programs I have used so far."
Robert Corbett PhD Candidate
Plant Physiology
Texas A&M University
"ChondroGene Ltd. has used the services of Gene Codes Corp. and their staff for about five years. As the sole person responsible for the sequencing department at ChondroGene, I feel no hesitation in relaying our good experiences with Gene Codes. They have always made them themselves easily available and proven themselves quite knowledgeable of their software products. In addition and more importantly, their product, Sequencher, has proven effective and has passed the test of time in this ever changing field."
James Loukides
Sequencing Department
ChondroGene Ltd.
"We have been relying on Sequencher since 1999, and we use it for everything from complete BAC shotgun assemblies to SNP discovery. The software is extremely user-friendly, and its graphical outputs are perfect for generating reports that we can present to our customers. Moreover, you don't have to be a Linux guru to make the application work, yet it is among the most powerful tools on the market. Overall, we are very pleased with this product, and we are happy to recommend it to our customers."
Ken Paynter
SeqWright
"My lab couldn't run without Sequencher. We depend on it! And I've always found that the people at Gene Codes are always willing to help with unusual situations and went the proverbial extra mile to help out.
"Throughout my graduate and postdoctoral research, I spent time in three different countries, and Sequencher was always the software of choice for sequence analysis. When I started to set up my own lab and research program, Sequencher was my first major purchase, as my lab simply could not run without it. Although I have tried other programs, they pale in comparison to the ease and efficiency of using Sequencher.
"I have found the customer service at Gene Codes to be excellent. Over the years, as operating systems and hardware have changed, Gene Codes has worked hard to upgrade.
"Although I operate a small lab and only own a single Sequencher license, I never felt that I was receiving anything but the best personal and prompt service."
Naomi M. Fast
Department of Botany
University of British Columbia
"We use Sequencher software to analyze and compare sequence data in candidate genes as part of our work to identify the genetic basis of a common birth defect. Sequencher software has played a vital role in the organization and analysis of our sequence data. The large number of assembly and trimming parameters has allowed us to identify SNPs thoroughly, efficiently, and accurately. The support staff has been an enormous help in teaching us ways to best utilize the software for the specific needs of our study."
Meaghan K. Russell
Department of Pediatric Surgery
Massachusetts General Hospital
"Gene Codes provides cutting edge software to deliver the bases to you!."
J. Robert Macey Ph.D
Merritt College