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HSLS MolBio Available Software

Bioinformatics software available to Pitt researchers.

About Sequencher

Next-Generation Sequencing:

  • The Sequencher interface helps you select options, set values, and learn the available functionality with descriptions and tool tips.
  • Perform SNP analysisMethylation analysis, or RNA tolerant alignment in just a few steps.
  • View your results in Tablet.
  • BWA, Velvet, Maq, GSNAP and Tablet are only the start for Sequencher.   If you are sequencing mixed populations, then combine the power of reference-guided-alignment with de novo assembly. Align reads to a reference and capture the unaligned reads for further rounds of reference-based alignment or de novo assembly.
  • With the addition of the Cufflinks suite you can perform RNA-Seq Differential Expression using the same style of interface we developed for all our NGS algorithms.
  • We also added the charts you would expect to see, such as the Volcano plot, so you can view the results without resorting to the command line. Because we know you have your own favourite aligners we don’t insist you use ours. As long as your aligner creates SAM or BAM as its output you are ready to explore your data with one of the most widely regarded RNA-Seq tools available.

Sanger Sequencing:

  • Sequencher makes traditional sequence assembly easy while keeping you in control.
  • Trim your sequences for poor quality data with ease. You can even maintain a library of trim criteria to make life even easier.
  • With intuitive controls you can select the best algorithm for your data including Assemble to Reference. And if you are working with multiple samples from different sources then automate the assembly using Assemble by Name.
  • Editing your data has never been simpler with tools to help you locate and deal with ambiguities, check for heterozygotes and move around your data.
  • Use confidence values to assist in trimming data, quality checks, and SNP detection to improve the quality of your results.

General Analysis:

  • Sequencher’s Reference Sequence is a powerful feature controlling numbering, features and much more. Use it in conjunction with the Variance Table and easily determine whether you are looking at known or unreported SNPs.
  • Align sequences directly from Sequencher’s project desktop using Clustal. You can even use Assemble by Name with Clustal when you have multiple samples from different sources.
  • Produce reports from your work. The PDF reports from the Variance Table are a great way to share your information, keep in your lab notebook or use in presentations.
  • Customize your workspace, control the position of your windows, and use labels to distinguish your sequences and contigs. Use motifs and highlighting to identify sequence regions. Maintain all your settings in templates so that you and your colleagues can work to the same Standard Operating Procedure.


  • Sequencher Connections represents a new approach to performing multiple analyses on sequences or groups of sequences. Connections has expanded the power of Sequencher by allowing you to set up “channels” on which different analyses using different parameters or databases can be run. By simultaneously running analyses on multiple sequences or groups of sequences on different channels at the same time, Sequencher Connections can increase the speed with which you get results.

Registration & Access Info

Register here

  • Must have Pitt email address
  • Limited to on-campus computers
  • Runs on PC & Mac

Technical Support