A series of pictures of different lab equipment associated with DNA processing.

Software for Analysis

Chromatogram Trace Viewers

These programs are limited in scope but serve a good purpose in evaluating the quality of data produced by allowing users to view the raw data associated with .ab1 files.

FinchTV (Windows/OSX)
From the makers of our data management system. Displays quality scores and much more. We really like the feature that links directly to NCBI for a BLAST search! What is more the application is FREE!

4Peaks (OSX Only)
Written to run natively on OSX and makes full use of the OSX interface. The application has lots of features and is more than just a “chromatogram viewer”. The best feature is the application is totally FREE! The same people have other OSX applications that might be useful for scientists.

ABI Seq Scape(Windows)
Another free viewer. This program is provided by the maker of the machine we run your samples on.

Chromas LITE (Windows Only)
This application will allow PC users to display, edit and print Applied Biosystems chromatogram files. You can even translate the sequence and reverse complement it! There is a ‘Pro’ version with more features.

Traceviewer(Windows/OSX/Linux)
This is a Java program that allows the reading of sequence traces from ABI or SCF files, the display of traces on white or black background and the display of Phred quality values as bars or numbers with one of three different color schemes. TraceViewer is free for academic users. Traceviewer for the Macintosh does not suffer from the same problem as Editview.

Contig Assembly and Sequence Alignment

These software packages can be used to view, edit, assemble, align, BLAST and even design primers. Some of the programs have phylogenetic analysis software built in as well! For more information, click on the links below.

Proprietary Software:

Proprietary software may cost more, but it also tends to be more current and offers long term and ongoing support.

Free and Open Source Software:

Free, customizable and often times you can examine the source code. These can also be difficult to find support for.

 

Analysis Software geared toward the interests of Evolutionary Analysis, Population Genetics, Phylogenetics and the like:

A List of Phylogeny Programs by Joe Felsenstein If you can’t find what you’re looking for in this comprehensive and exhaustive list, it probably doesn’t exist.

A list of of Phylogeny Programs by Sergios-Orestis Kolokotronis

JMATING a software for the analysis of sexual selection and sexual isolation effects from mating frequency data.

Mesquite is software for evolutionary biology, designed to help biologists analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis.

TREEFINDER is a software to compute phylogenetic trees from molecular sequences.

TreeRot is a very easy program to use for determining Bremer indices (decay indices) for phylogenetic trees. It is also capable of providing partitioned DI, and after your analysis is complete, the program can parse your output log and give you the DI at each node (so you don’t have to go through the log file yourself and do the arithmetic).

SGRunner SG Runner is a graphical user interface for Seq-Gen.

Cadence Cadence helps to conduct Bayesian relative rates tests.

PolypSizer A program for measuring things. Very useful when combined with a digitizing pad and drawing tube.

Gel Reader A program for estimating band sizes on electrophoretic gels.

For Windows:

Acquity 4.0 (ccg12 and ccg13)

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MrBayes 3.0b4

Clustalx 1.83

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PAUP 4.0

DnaSP 4.0

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Phylip 3.65

GenePix Pro 6.0 (ccg12 and ccg13)

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Phyml 2.4.4

Genespring 7.2 (ccg12 and ccg13)

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Seq Scape 2.1.1

Mega 2

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Sequencing Analysis 5.1.1

Mega 3.1

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TreeView

For Macs:

Clustalx 1.83.1

MacClade 4.06

MrBayes 3.1.2

PAUP 4.0

Phylip 3.65

Phyml 2.4.4

TreeView 1.6.6

CoMET (Continuous-character Model Evaluation and Testing) is a Mesquite module for calculating the likelihood of different Brownian motion-based models of continuous character change on phylogenies

Modeltest A tool to select the best-fit model of nucleotide substitution

MrAIC Perl script for selecting DNA substitution models using PHYML

MrModeltest C program for selecting DNA substitution models using PAUP Mailfit: Perl script that runs PAUP and MrModeltest2 (or Modeltest) and sends (optionally) results via e-mail

Burntrees Perl script for manipulating MrBayes tree and parameter files. The script comes with an extra tool, catmb.pl, for concatenating files from separate MrBayes runs.

Vim Nexus syntax highlighting Nexus syntax highlighting files for the Vim editor. Recognizes many/most of the PAUP/MrBayes commands

Vim Nexus syntax highlighting Vim highlighting files for DNA sequence alignments

MrModelfit/Modelfit Perl script for running MrModeltest2/Modeltest

BootPHYML Perl script for performing non-parametric bootstrapping using PHYML