Open Source Tools

Mac OS X:

  • Dendroscope: A phylogenetic tree viewer with good graphics and the ability to generate many customized views of trees.
  • TreeFinder: A phylogenetic tool for displaying and viewing trees with good graphics and the ability to generate many customized views of trees. Only a G4 or G5 version available, not for Intel Macs.
  • Mauve: Mauve is a genome wide alignment tool, particularly useful for multiple alignments of fully sequenced bacterial genomes.
  • CellDesigner : A tool for importing or drawing de novo representations of gene regulatory or biological pathways.
  • GENtle: A DNA analysis software tool, modeled on Vector NTI, very basic functionality.
  • PHYLIP: PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). Only a command line interface is currently available.
  • Mr Bayes: MrBayes is a program for the Bayesian estimation of phylogeny.
    Only a command line interface is currently available.
  • CLC Free Workbench 4.0: Contains many bioinformatics tools and should primarily be considered for Mac OS X 10.4 users as a partial alternative to Vector NTI.
  • Ridom Trace Editor: A chromatograph viewer and editor. We suggest this for Mac OS X 10.4 users. Other trace viewing tools are available for PC or older Mac OS X systems.
  • ClustalX: ClustalX is a new windows interface for the ClustalW multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analyzing the results. This program allows you to create Neighbor Joining trees with bootstrapping. Currently the most recent version for the Mac is "clustalx1.83.MAC.sea.Hqx"
  • Njplot: Njplot is for viewing trees created by programs such as ClustalX, it is sort of primitive but it will display bootstrapping values.
  • Treeview X: Treeview X (not to be confused with Java Treeview for viewing microarray analysis results) is a better tree viewer than NJplot visually, but will not show the bootstrapping values that may have been generated with any phylogenetic program.
  •  4Peaks: 4Peaks is a program allows viewing and editing of sequencing files as well as visualization of trace data and phred quality data. 4Peaks supports many file formats including ABI, SCF, and ZTR.
  • FinchTV: FinchTV is another free chromatogram viewer and sequence editor. FinchTV supports ABI and SCF formats and allows sequence searching using regular expressions.
  • Cluster 3.0: Cluster can be used to perform Hierarchical and K-Means clustering operations as well as generating Self Organizing Maps and Principle Component Analyses. Cluster 3.0 also allows clustering by genes based on many different experiments or by the experiments themselves. The output of Cluster 3.0 can be viewed with Java Treeview (listed below).
  •  Java Treeview: Java Treeview is an open source java-based tool for visualizing gene expression data and the results of clustering operations performed by external programs such as Cluster (listed above). Java Treeview supports expression data in the generalized CDT file format and cluster tree files in gene tree rows (.gtr) and array tree rows (.atr) formats.
  • DeepView: DeepView is a freeware program that allows viewing and analysis of three-dimensional molecules in the PDB format.
  • EMBOSS: EMBOSS is a comprehensive suite of sequence analysis tools. It is available for download to your local machine but it can also be run through your UNC isis account. To run the software remotely, SSH to isis.unc.edu and log in. At the prompt, type ipm add emboss-280. You should now be able to run all programs included in the EMBOSS package.
  • Argo: Argo is a free java-based genome browser that allows users to graphically view sequence and annotation tracks. Argo allows for a great deal of customization and supports many different file types, including FASTA, Genbank, Genscan, BLAST and GFF.
  • TextWrangler: A text editing tool. A text editor is a tool for simply editing text. You can use a text editor for a wide variety of tasks from cleaning up data, to editing files on your Mac, to writing HTML or coding.

Windows:

  • MEGA: MEGA (Molecular Evolutionary Genetic Analysis) is a desktop tool for performing a variety of common phylogenetic analyses and for viewing and manipulating the resulting phylogenetic trees.
  • Glimmer: Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA.
  • Mauve: Mauve is a genome wide alignment tool, particularly useful for multiple alignments of fully sequenced bacterial genomes.
  • M-GCAT: M-GCAT is a large scale alignment tool geared toward examining synteny at the bacterial genome/chromosome level; for closely related species only. Does not work well for sequences that do not have significant homology.
  • Treeview X: Treeview X (not to be confused with Java Treeview for viewing microarray analysis results) is a better tree viewer than NJplot visually, but will not show the bootstrapping values that may have been generated with any phylogenetic program.
  • PHYLIP: PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). Only a command line interface is currently available.
  • Mr Bayes: MrBayes is a program for the Bayesian estimation of phylogeny.
    Only a command line interface is currently available.
  • Dendroscope: A phylogenetic tree viewer with good graphics and the ability to generate many customized views of trees.
  • TreeFinder: A phylogenetic tool for displaying and viewing trees with good graphics and the ability to generate many customized views of trees.
  • Genedoc: Genedoc is for viewing DNA and protein sequence alignments, good for visualization and manipulating the color of alignments.
  • Ghostscript 8.64 and GSView 4.9: These are for viewing postscript files, such as for viewing the trees you make in the NC Bioportal ( the .ps files). Both programs need to be installed.
  • ClustalX: ClustalX is a new windows interface for the ClustalW multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analyzing the results. This program allows you to create Neighbor Joining trees with bootstrapping. Currently the most recent version for Windows is "clustalx1.83.zip".
  • FinchTV: FinchTV is another free chromatogram viewer and sequence editor. FinchTV supports ABI and SCF formats and allows sequence searching using regular expressions.
  • Cluster 3.0: Cluster can be used to perform Hierarchical and K-Means clustering operations as well as generating Self Organizing Maps and Principle Component Analyses. Cluster 3.0 also allows clustering by genes based on many different experiments or by the experiments themselves. The output of Cluster 3.0 can be viewed with Java Treeview (listed below).
  • Java Treeview: Java Treeview is an open source java-based tool for visualizing gene expression data and the results of clustering operations performed by external programs such as Cluster (listed above). Java Treeview supports expression data in the generalized CDT file format and cluster tree files in gene tree rows (.gtr) and array tree rows (.atr) formats.
  • DeepView: DeepView is a freeware program that allows viewing and analysis of three-dimensional molecules in the PDB format.
  • BioEdit: BioEdit is a fairly comprehensive sequence alignment and analysis tool. BioEdit supports a wide array of file types and offers a simple interface for local BLAST searches.
  • EMBOSS: EMBOSS is a comprehensive suite of sequence analysis tools. It is available for download to your local machine but it can also be run through your UNC isis account. To run the software remotely, SSH to isis.unc.edu and log in. At the prompt, type ipm add emboss-280. You should now be able to run all programs included in the EMBOSS package.
  • Argo: Argo is a free java-based genome browser that allows users to graphically view sequence and annotation tracks. Argo allows for a great deal of customization and supports many different file types, including FASTA, Genbank, Genscan, BLAST and GFF.
  • TextPad: A text editing tool. A text editor is a tool for simply editing text. This has much more functionality than either Wordpad or Notepad, and is especially good for opening and examining large genomic level data files.
  • CellDesigner: A tool for importing or drawing de novo representations of gene regulatory or biological pathways.
  • GENtle: A DNA analysis software tool, modeled on Vector NTI, very basic functionality.

Web or Java Tools (platform independent):

  • Ensembl: Genome Browser, primarily for completed metazoan genomes with annotation. Also contains BioMart, a tool for custom querying and retrieval of genome scale datasets.

  • UCSC Genome Browser: Comparable to Ensembl, for displaying annotations of completed genomes. Also useful for uploading and displaying large setsuser data and for custom querying and retrieval of genome scale datasets.

  • HapMap: Genome Browser for accessing SNP data and genotyped SNP datasets from the HapMap projects. Also for viewing LD and haplotype structure of SNPs in the context of gene annotation.

  • BioMart: For generating custom queries and downloading datasets from completed genomes. Can also access this function through Ensembl. The HapMap website has a similar function (HapMart) for queries of SNP datasets.

  • Haploview: Haploview is a tool for examining LD (linkage disequilibrium) and haplotype structure of the human genome based on the HapMap populations. Also useful for determining tag SNPs.
  • Mobyle: Mobyle is a portal containing many commonly used EMBOSS tools, including tools for DNA and protein analysis, sequence alignment, assembly, and phylogenetic analysis.
  • Oslo Bioportal: The University of Oslo Bioportal is a site that is largely focused on phylogenetic analysis tools. Some of these applications are computationally intensive and it is advisable to submit them remotely to a site such as this.
  • CBSU Web Computing Resources: The Computation Biology Service Unit (CBSU) at Cornell University maintains a selection of commonly used bioinformatics tools available for use within their compute cluster. Many of these are parallelized versions of stand alone tools such as clustalw, t-coffee, and Mr Bayes which can be computationally intensive and are often best done at a remote site such as this. Some applications available here are available to the public, some only to users at Cornell.
  • JalView: A tool for editing and viewing for multiple sequence alignments.
  • jMODELTEST: A java version of MODELTEST for determining the best fit model of nucleotide substitution for a given dataset prior to phylogenetic analysis.
  • FindModel:This is an online version of ModelTest, a tool used for determining the appropriate distance model for a set of nucleotide sequences to be used in a phylogenetic analysis. This link is to a webpage for an online version of this tool.
  • TCoffee: A multiple sequence alignment tool; an alternative to clustalw but generates an alignment in a clustalw format (.aln) that is a useful starting point for phylogenetic analysis. This link is to a webpage for an online T coffee tool.
  • Phylemon : An online version of a variety of common programs for evolutionary analysis including phylogenetic analysis (PHYLIP, PhyML, TreePuzzle, Mr Bayes) multiple sequence alignment (ClustalW, Muscle) and a variety of evolutionary tests. This site is still being developed, not all of these tools currently function.
  • Galaxy: The Galaxy website contains many text editing, manipulation, and file conversion tools that are appropriate for large genome-scale data files, such as those one might download from the UCSC Browser or published chIP-chip experiments.
  • Readseq: A tool for converting between common sequence file formats, particularly useful for those using various phylogenetic analysis tools.