Jongsik Chun of the School of Biological Sciences, Seoul National University, Korea (jchun  (at) snu.ac.kr) has released PHYDIT version 3.1. PHYDIT is a sequence alignment environment that can align either nucleotide or protein sequences manually or using pairwise methods, and contains some PHYLIP programs to do either neighbor-joining or least-squares phylogenies on the alignments. PHYDIT is available as a Windows executable. It is available free for noncommercial use. The user needs to register to download. The PHYDIT web page is http://plaza.snu.ac.kr/~jchun/phydit/.

Don Gilbert (gilbertd  (at) indiana.edu) of the Department of Biology of the University of Indiana, has written SeqPup versions 0.9 and 0.6, a biological sequence editor and analysis program usable on MacOS, Windows and Unix systems. It allows alignment of sequences by hand and submission of selected parts of selected sequences to phylogeny programs, as well as to network services such as BLAST. It is available in a more complete earlier version (0.7) written in C++, or a later (0.9) version written in Java. The latter will work on all systems that have the Java 1.1 runtime environment. It will not work on the Java 1.2 runtime environment, so the earlier Java 1.1 environment needs to be installed as well if the later version of Java is present. (I do not know whether SeqPup works with later versions of Java). The two versions of SeqPup are described at a web page at http://iubio.bio.indiana.edu/soft/molbio/seqpup/java/seqpup-doc.html. Versions 0.9 and 0.6 can be obtained at its download web page The earlier version (0.6) is available in C++, and executables of it are available for MacOS (the PowerMac and 68K platforms), Windows, and Unix X windows systems including Sun Solaris, SGI Irix, Dec (HP/Compaq) Unix, Linux. The C++ source code for the 0.6 version is available by anonymous ftp at: iubio.bio.indiana.edu in directory util/dclap/source/.

  Matthias Wolf, Joachim Friedrich, Thomas Dandekar, and Tobias Müller of the Department of Bioinformatics at the the Biocenter, University of Würzburg, Germany (Matthias.Wolf (at) biozentrum.uni-wuerzburg.de) have written CBCAnalyzer versions 1.0.3 and 1.1β, programs for inferring phylogenies based on compensatory base changes (CBCs). The CBCAnalyzer (CBC = compensatory base change) is a custom written software toolbox consisting of three parts, CTTransform, CBCDetect, and CBCTree. CTTransform reads several CT-file formats (ct, RNAviz ct or Mac ct), and generates a so called "bracket-dot-bracket" format that specifies which sites are paired in an RNA structure. This typically is used as input for other tools such as RNAforester, RNAmovie or MARNA. The latter one creates a multiple alignment based on primary sequences and secondary structures that now can be used as input for CBCDetect. The count (distance) matrix of compensating changes obtained by CBCDetect is used as input for CBCTree that reconstructs a phylogram by using the BIONJ algorithm. It is described in the paper: Wolf, M., J. Friedrich, T. Dandekar and T. Müller. 2005. CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures. In Silico Biology 5: 0027. It is available as C++ source code which can be compiled on Linux, and as Windows executables. It can be downloaded from its web site at http://cbcanalyzer.bioapps.biozentrum.uni-wuerzburg.de/

Wolfgang Ludwig and Oliver Strunk of the Lehrstuhl für Mikrobiologie of the Technische Universität München (wolfgang.ludwig  (at) arb-home.de) distribute ARB, an environment for 16s/18s/23s ribosomal RNA sequence data. It provides a windowing environment for building up databases of RNA sequences, aligning them, and searching, editing, modifying, aligning, profiling, and constructing trees. ARB uses its own RNA sequence databases which are made available to ARB over the Web. For phylogenies it uses programs from PHYLIP, AXML, PHYML and fastDNAml, as well as its own ARB Neighbor-Joining program. ARB is also incorporates a variety of other sequence analysis software. It can handle large numbers of sequences and has sophisticated tree drawing and manipulation. ARB is distributed as source code and executables for Linux systems, specifically Ubuntu and SuSE Linux. It can also be compiled successfully on SunOS and Mac OS X. ARB is available from its web site at http://www.arb-home.de/. A Mac OS X port of ARB is available by Mike Dyall-Smith of the Max Planck Institute of Biochemistry at http://www.haloarchaea.com/resources/arb/index.html.

Ian Holmes of the Department of Bioengineering of the University of California at Berkeley, Berkeley, Calfornia (ihh (at) berkeley.edu) has released DART (Dna, Amino and Rna Tests), a package of programs to do a variety of genomic, alignment, and RNA structure inferences. (DART is not to be confused with NCBI's Domain Architecture Retrieval Tool, also called DART). Various programs in the DART package do phylogenetic alignment; RNA structure prediction and multiple RNA alignment, stochastic context-free grammars, inference of evolutionary models, phylo-HMMs and phylo grammars, reconstruction of ancestral sequences; and phylogenomics. It contains a number of programs including

• stemloc and EvolDeeds for RNA alignment and ancestral prediction
• xrate for phylo-grammars
• phylocomposer and phylodirector for analysis and visualization
• other statistical alignment programs in the Handel package
• simgenome for simulation of genome sequence alignments

Andrew Smith, Thomas W. H. Lui and Elisabeth Tillier of the Ontario Cancer Institute and the Department of Medical Biophysics at the University of Toronto, Canada (e.tillier (at) utoronto.ca) have released rRNA phylogeny, a program package to infer phylogenies from ribosomal RNA using a model of substitution that allows for compensating substiutions at paired sites. The program makes use of a model (the OTRNA model) of ribosomal RNA substitution that has different rates for paired and unpaired sites, that reflect the lower probability of a compensated substitution that maintains the pairing. The model is empirically tabulated from rRNA sequences and used in a modified version of programs from PHYLIP to infer phylogenies. The package also allows distances to be computed from the OTRNA model for use in distance matrix programs. The methods are described in the paper: Smith, A., T. W. H. Lui and E. R. M. Tillier, 2004. Empirical substitution models for Ribosomal RNA Molecular Biology and Evolution 21: 419-427. It is available as C source code, Windows executables and Linux executables. It can be downloaded from its web site at http://www.uhnresearch.ca/labs/tillier/software.htm

Dick Hwang and Phil Green of the Department of Genome Sciences of the University of Washington, Seattle, Washington (dhwang (at) u.washington.edu) has released AMBIORE (Applications for Mcmc Bayesian Inference Of Rates in Evolution), version 1.00, which estimates rates of change in nucleotide sequences depending on the two neighboring bases. It implements a flexible and computationally efficient Bayesian Markov chain Monte Carlo approach to estimating rates in evolution given a sequence alignment and tree topology relating the species. The evolutionary model allows substitution rates at a site to depend on the two flanking nucleotides, the branch of the phylogenetic tree, and position within a sequence. The methods are described in the paper: Hwang D. G. and P. Green. 2004. Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proceedings of the National Academy of Sciences U.S.A. 101: 13994-14001. It is available as C source code. It can be downloaded from its web site at http://www.phrap.org/othersoftware.html

Chris Saunders, then of the Department of Genome Sciences of the University of Washington, Seattle, Washington (and currently at Illumina, Inc.) has written CodeAxe version 1.0, a tool for the phylogenetic analysis of mutation and selection in coding sequences. It provides, for a phylogeny provided by the user, analysis of approximate maximum likelihood nucleotide, codon and "extended codon" models that allow for neighbor-dependent nucleotide mutation, asymmetric exchange-dependent amino acid selection, nonreversible evolution and mixture models of mutation and selection classes. It is described in the paper: Saunders, C. T. and P. Green. 2007. Insights from modeling protein evolution with context-dependent mutation and asymmetric amino acid selection. Molecular Biology and Evolution 24(12): 2632-2647. It is available as C++ source code. It can be downloaded from its web site at http://www.phrap.org/othersoftware.html

Tom Hall, then of the Department of Microbiology at North Carolina State University, and now of Ibis Therapeutics, Carlsbad, Calfornia (thall  (at) isisph.com) has produced BioEdit, version 7.0.5. This is a sequence editor with many kinds of general molecular biology functions available (alignment, BLAST searches, plasmid drawing, restriction mapping, sequence machine trace viewing, etc.). For our purposes the feature worth mentioning is that it comes with a number of existing phylogeny programs which can be automatically run from within BioEdit. These are: TreeView, fastDNAml, and six DNA and protein programs from PHYLIP. It has been described in the paper: Hall, T. A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Sympoisum Series 41: 95-98. BioEdit is available as Windows executables. Version 7.0.5 is available from its web site at http://www.mbio.ncsu.edu/BioEdit/bioedit.html.

  GeneStudio, Inc. of Suwanee, Georgia (info  (at) genestudio.com) has released GeneStudio Pro, version 2.1.2.4, a commercial package for sequence analysis and sequence format conversion. (Incidentally, although the Suwanee River is partly located in Georgia, the town of Suwanee is not located "way down upon the Suwanee River" but is quite far from it). Included is an Alignment Editor that can invoke a variety of phylogeny programs, including fastDNAml, some programs from PHYLIP, Tree-puzzle and TreeView. It can also do many other functions such as sequence format conversion, BLAST searches, and contig editing. GeneStudio Pro is for the Windows platform. A free trial version is available. Prices are not given on their web site but are available on request from a page on their web site, accessed through the trial version. For further information see the GeneStudio Pro web site at http://www.genestudio.com/genestudio.htm.

  Stuart Ray, of the Division of Infectious Diseases of the Department of Medicine at the Johns Hopkins University School of Medicine, Baltimore, Maryland (sray (at) jhmi.edu) has produced Simplot, version 3.5.1. It is a Windows program that serves as a front end to either code from PHYLIP or to PAUP* and enables you to easily submit jobs to them. SIMPLOT enables you to select regions and do other forms of data selection. It can also carry out the "bootscanning" method of detecting inconsistencies in trees in different regions of a sequence, which can be a signal for recombination. It was first described in the paper: Lole, K. S., R. C. Bollinger, R. S. Paranjape, D. Gadkari, S. S. Kulkarni, M. G. Novak, R. Ingersoll, H. W. Sheppard, and S. C. Ray. 1999. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. Journal of Virology 73(1): 152-160. It is distributed as a Windows executable through its web site at http://sray.med.som.jhmi.edu/SCRoftware/simplot/

James J. Cai of the Department of the Department of Veterinary Integrative Biosciences at the Texas A&M University, College Station, Texas (jcai (at) tamu.edu) has written MBEToolbox (Molecular Biology and Evolution Toolbox), version 2.21, A MATLAB package to enable evolutionary biologists to analyze and view DNA and protein sequences. MBEToolbox includes sequence manipulation and statistics, evolutionary distance calculations, tree creation, a novel window analysis method and a graphical user interface. version 2.0 added new functions for phylogenetic analyses by the maximum likelihood method, analysis of site-specific evolutionary rates, and algorithms to detect recombination. It is described in the papers:

• Cai, J. J., D. K. Smith, X. Xia, and K.-Y. Yuen. 2005. MBEToolbox: a Matlab toolbox for sequence data analysis in molecular biology and evolution. BMC Bioinformatics 6: 64 (22Mar2005)
• Cai, J. J., D. K Smith, X. Xia, and K.-Y. Yuen. 2006. MBEToolbox 2.0: An enhanced version of a MATLAB toolbox for Molecular Biology and Evolution. Evolutionary Bioinformatics Online 2: 189-192.

  Salvador Ramirez of the Departamento de Oceanografia of the Universidad de Concepcion, Chile (sram (at) profc.udec.cl) has released Bosque Phylogenetic Analysis Software, version 1.7.42, an integrated set of phylogenetic analysis software into a complete graphical user interface. Bosque is a graphical program that integrates console programs from the PHYLIP package, from TREE-PUZZLE, and from MUSCLE. As a graphical program it also includes sequence, alignment and tree editors to ease the manipulation of the data, the execution of the programs and the administration of the output result from the phylogenetic programs. It also has the option to function as a client-server program where a Bosque server is installed, thus allowing the remote execution of the mentioned phylogenetic programs. It is available as Windows executables, Mac OS X executables, and Linux executables. It can be downloaded from its web site at http://bosque.udec.cl

John Archer and David Robertson of the Faculty of Life Sciences of the University of Manchester (john.archer.jpa (at) googlemail.com) and Andrew Rambaut of the Institute of Evolutionary Biology of the University of Edinburgh (a.rambaut (at) ed.ac.uk) have produced Segminator II, a tool for extracting data from reads from viral data generated using the 454 Life Science sequencing platform. Following the mapping and pairwise alignment of reads, data that is immediately accessible in tabulated format includes:

1. Obtaining nucleotide and amino acid residue frequencies at sites across the template.
2. Generating a consensus across data set using overlapping windows (while allowing for indels differing from those in relation to the template).
3. Removal of reads based on hamming distance cutoff thresholds.
4. Reads spanning a particular region of the template can be multiply aligned and used to infer phylogenetic trees. and
5. Identification of variants within viral populations.

   John Archibald and Andrew Roger, of the Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada (john.archibald (at) dal.ca and aroger (at) is.dal.ca) have released Likewind version 1.0.1. This is a set of three Perl scripts that allow the user to create the necessary PAUP* blocks to drive a likelihood analysis of differences in phylogenies betweend different parts of a molecule. The object is to detect recombination, hybridization, or other sources of conflicting phylogenetic signal. The utilities also harvest the output from PAUP* and present it to the user as a log-likelihood difference plot. This shows the log-likelihood difference in the window of adjacent sites between a predefined tree and the best estimate from the local information. The scripts need Seq-Gen and PAUP* present in a Linux or Unix environment. The method has been described in a paper: Archibald, J. M. and A. J. Roger. 2002. Gene conversion and the evolution of euryarchaeal chaperonins: a maximum likelihood-based method for detecting conflicting phylogenetic signals. Journal of Molecular Evolution 55: 232-245. Likewind is available from its web site at http://rogerlab.biochemistryandmolecularbiology.dal.ca/Software/Software.htm#likewind

Christian Zmasek, currently of the Genomics Institute of the Novartis Research Foundation in San Diego, California (czmasek  (at) gnf.org) and Sean Eddy (eddy  (at)  genetics.wustl.edu) of the Department of Genetics, Washington University, St. Louis, Missouri have released FORESTER, version 1.92, a package of Java routines for inferring gene function using the output of high-throughput genome sequencing. It includes the RIO Resampled Inference of Orthologs method which searches for orthologs in the PFAM database, the SDI Speciation-Duplication Inference method, and ATV, a tree viewer. This can take a tree in the standard Newick format (and also in an extension that has additional information), and display it in various forms. These are described in papers:

• Zmasek, C.M. and S. R. Eddy. 2001. ATV: display and manipulation of annotated phylogenetic trees. Bioinformatics 17: 383-384.
• Zmasek, C. M. and S. R. Eddy. 2001. A simple algorithm to infer gene duplication and speciation events on a gene tree. Bioinformatics 17: 821-828.
• Zmasek, C. M. and S. R. Eddy. 2002. RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinformatics 3: 14.

Louxin Zhang (matzix  (at) nus.edu.sg) of the Department of Mathematics of the Faculty of Science, of the National University of Singapore has produced WebPHYLIP, version 2.0, a web interface for the PHYLIP package, which can submit jobs to it. It has been described in an article: Lim, A. and L. Zhang. 1999. WebPHYLIP: a web interface to PHYLIP. Bioinformatics 15(12): 1068-1069. There are versions as Windows executables and for Linux/Unix as C source code which can be compiled. It is available at this download page at http://www.math.nus.edu.sg/~matzlx/webphylip_download/ above address.

  Biomatters, Ltd. in Auckald, New Zealand (sales (at) geneious.com) has released Geneious version 5.3, a Java package for sequence management, searching, editing and phylogenies. Geneious is an integrated bioinformatics tool suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information, publications, etc. It features tree-based progressive sequence alignment and phylogenetic analysis by Neighbor-Joining and UPGMA, bootstapping, drawing the phylogeny, access to biological databases, BLAST, protein structure viewing, NCBI, EMBL, PubMed auto-find, and more. It includes an API for creating your own plugins. It is available as Java executables. Geneious is available for free; that version cannot edit sequences or annotations, cannot run the multiple alignment program ClustalW from within Geneious, and cannot do some other tasks. A full version, Geneious Pro, is available commercially. Free downloads of Geneious or purchases of Geneious Pro can be done from the Biomatters web site at http://www.biomatters.com. Geneious Pro is available from Biomatters, Ltd. for a 12-month license for academic or government institutions for $395, for a 12-month student license for $175, or for a 12-month commercial license for $995. The prices for perpetual licenses for these classes of users are $795, $395, and $1,995. Discount prices for multiuser licenses are also available. Additional plugins enabling it to run MrBayes, PAUP* (Geneious Pro only), PHYML, DualBrothers, and MAFFT are available free at the website.

Catherine Letondal of the Institute Pasteur, Paris, France (letondal (at) pasteur.fr) distributes PISE (Pasteur Institute Software Environment), a tool to generate Web interfaces for Molecular Biology programs. PISE allows the user to generate web page interfaces to many programs, including PHYLIP, EMBOSS, MOLPHY, and fastDNAML, Web interfaces for these are available in PISE. The web interfaces allow you to rapidly create a web server for running these programs. PISE is used to create the Pasteur Institute web server. PISE web servers allow the results of one program to the "piped" to another program. The web server generated is designed to be run on a Unix machine. It is described in the paper: Letondal C. 2001. A Web interface generator for molecular biology programs in Unix. Bioinformatics, 17(1): 73-82. It is available as Perl scripts. It can be downloaded from its web site at http://www.pasteur.fr/recherche/unites/sis/Pise/

MathWorks of Natick, Massachusetts have produced Bioinformatics Toolbox version 3.6, a MATLAB toolbox for bioinformatics. It has many functions for sequence analysis and microarray data, including multiple sequence alignment and consensus sequences. For this listing, the relevant ones are that it enables you to create and edit phylogenetic trees. You can calculate pairwise distances between aligned or unaligned nucleotide or amino acid sequences using a broad range of similarity metrics, such as Jukes-Cantor, p-distance, alignment-score, or a user-defined distance method. Phylogenetic trees are constructed using hierarchical linkage with a variety of techniques, including neighbor joining, single and complete linkage, and UPGMA. Bioinformatics Toolbox includes tools for weighting and rerooting trees, calculating subtrees, and calculating canonical forms of trees. Through the graphical user interface, you can prune, reorder, and rename branches; explore distances; and read or write Newick-formatted files. You can also use the annotation tools in MATLAB to create presentation-quality trees. It is available as a MATLAB package. It is available from MathWorks, Inc. The price is not available on the website without a login, but there are Commercial, Academic, and Student prices. It us believed that commercial licenses are about $1,000, academic licenses about $90. More information and sales contact can be obtained from the product web site at http://www.mathworks.com/products/bioinfo/

 The UGENE team of the Unipro company, Novosibirsk, Russia (mfursov (at) unipro.ru) has released UGENE version 1.8.0, a free cross-platform genome analysis suite. It is a sequence manipulation environment which can call other programs as plugins, including PHYLIP programs to compute distances and create trees from distance matrix methods, and MUSCLE to align sequences. It can also plot trees. It is available as C++ source code, Windows executables, Linux executables, Powermac Mac OS X executables and Intel Mac OS X executables. It can be downloaded from its web site at http://ugene.unipro.ru

   Andrew Rambaut of the Institute of Evolutionary Biology of the University of Edinburgh, Edinburgh, Scotland (a.rambaut (at) ed.ac.uk) has written Phylogen version 1.1, a tree simulation program. It simulates phylogenies produced by a birth-death process. It also has a mode that allows for multiple epdisodes of evolution and multiple mass extinctions. It is available as generic source code for Unix and as Mac OS, Mac OS X, and Windows executables. It is distributed from its web page at http://tree.bio.ed.ac.uk/software/phylogen/. Although Rambaut considers it to have superseded his earlier program Bi-De. Phylogen is itself now unsupported software that will be distributed but not developed further.

Oliver Pybus, of the Department of Zoology, University of Oxford, (oliver.pybus  (at) zoo.ox.ac.uk and Andrew Rambaut, of the Institute of Evolutionary Biology of the University of Edinburgh, Edinburgh, Scotland (a.rambaut (at) ed.ac.uk) have written Genie (GENealogical Interval Explorer) version 3.0, a program for the inference of demographic history from reconstructed phylogenies. The methods it implements are described in the papers:

• Pybus, O., A. Rambaut and P. Harvey. 2000. An integrated framework for the inference of viral population history from reconstructed genealogies. Genetics 155: 1429-1437.
• Pybus, O. G., M. A. Charleston, S. Gupta, A. Rambaut, E. C. Holmes, and P. H. Harvey. 2001. The epidemic behavior of the Hepatitis C Virus. Science 292: 2323-2325.
• Strimmer, K. and O. G. Pybus. 2001. Exploring the demographic history of DNA sequences using the generalised skyline plot. Molecular Biology and Evolution 18: 2298-2305.

Paul-Michael Agapow (p.agapow  (at) ic.ac.uk) and Nick Isaac, then of the Department of Biology, Imperial College, Silwood Park, U.K. (and most recently of the Health Protection Agency, U.K.) has released MacroCAIC version 1.0.1, which was developed from CAIC, by Andy Purvis and Andrew Rambaut. MacroCAIC uses phylogenies and data sets of character values to examine correlates of species richness, i.e. which traits are associated with abnormal speciation. The phylogeny is used to make these correlations independent. Traits may be continuous or discrete, and not every trait value needs to be known for every clade in the phylogeny. MacroCAIC has been described in a paper: Agapow, P.-M. and N. J. B. Isaac. 2002. MacroCAIC: correlates of species richness. Diversity & Distributions 8: 41-43. MacroCAIC is a PowerMac and 68k Mac binary executable for Mac OS. It is available from its web site at http://www.bio.ic.ac.uk/evolve/software/macrocaic/index.html.

   Andrew Rambaut, of the Institute of Evolutionary Biology of the University of Edinburgh, Edinburgh, Scotland (a.rambaut (at) ed.ac.uk) University of Oxford, (andrew.rambaut  (at) zoo.ox.ac.uk) and Nick Grassly of the Department of Infectious Disease Epidemiology of Imperial College School of Medicine, St. Mary's Campus, London (n.grassly  (at) ic.ac.uk) have written Seq-Gen (Sequence Generator), version 1.3.2, a program that will simulate the evolution of nucleotide sequences and protein sequences along a phylogeny or multiple phylogenies, using common models of the nucleotide or protein substitution process. A range of models of molecular evolution are implemented Nucleotide frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. The models available are the Hasegawa, Kishino and Yano (HKY) model, the Felsenstein F84 model, the general reversible model, the Kimura 2-parameter model, the Jukes-Cantor model and the Dayhoff PAM, JTT, Blosum62, mtREV, and WAG amino acid substitution models. Rate heterogeneity among sites or among the different positions within a codon can be specified. Seq-Gen is described in a paper: Rambaut, A. and N. C. Grassly. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Computer Applications in the Biosciences ICABIOS) 13: 235-238. A Mac OS executable is available, as well as source code files for Unix systems. A Windows executable is available for an earlier version, 1.3.1. These are available from its Web page at http://tree.bio.ed.ac.uk/software/seqgen/.

  Tom Wilcox has written SG Runner version 2.0.1, a graphical user interface for running Seq-Gen. It is available as Powermac Mac OS X executables. It can be downloaded from his software web site at http://homepage.mac.com/tpwilcox/FileSharing15.html

Nick Grassly of the Department of Infectious Disease Epidemiology of Imperial College School of Medicine, St. Mary's Campus, London (n.grassly  (at) ic.ac.uk) and Andrew Rambaut, of the Institute of Evolutionary Biology of the University of Edinburgh, Edinburgh, Scotland (a.rambaut (at) ed.ac.uk) have written PSeq-Gen (Protein-Sequence Generator), version 1.1, which will simulate the evolution of protein sequences along evolutionary trees. Three common models of amino acid substitution are implemented (PAM, JTT, and mtREV), allow for user-defined amino acid frequencies. Site-specific rate heterogeneity following a gamma distribution is allowed. The program can handle multiple trees and produce multiple data sets. PSeq-Gen is available from a web site at the IUBIO server at http://iubio.bio.indiana.edu/soft/iubionew/molbio/evolution/phylo/PSeq-Gen/main.html as Unix source code and also as Mac OS executables. An online manual can also be viewed at that site. PSeq-Gen is now largely superseded by Seq-Gen, and although it is still available at the IUBIO server it is not being actively supported by its authors.

Nick Grassly, of the School of Public Health of Imperial College, St. Mary's Campus, London (n.grassly (at) imperial.ac.uk) and Andrew Rambaut, of the Institute of Evolutionary Biology of the University of Edinburgh, Edinburgh, Scotland (a.rambaut (at) ed.ac.uk) wrote Treevolve, version 1.32 and also Ptreevolve, programs that simulate the evolution of DNA and protein sequences respectively. The molecular sequences are simulated under coalescent models with constant population size, or with exponential population size growth. In addition different levels of recombination can be specified. In Treevolve, it is also possible to have an island model of population subdivision. Treevolve and Ptreevolve are written in ANSI C and should compile on most Unix systems. They are also available as Mac OS executables, and a project file for the MetroWerks Codewarrior compiler is included in the Macintosh archive. They can be obtained from programs viewed, from their archives at the IUBIO web site at http://microbe.bio.indiana.edu:7131/soft/iubionew/molbio/genetic/pop/TreeVolve/

Jens Stoye, Dirk Evers and Folker Meyer of the Research Center for Interdisciplinary Studies on Structure Formation (FSPM) and the Technische Fakultät of the University of Bielefeld, Germany (j.stoye  (at) dkfz-heidelberg.de, dirk  (at)  TechFak.Uni-Bielefeld.de, and folker  (at)  TechFak.Uni-Bielefeld.de) have released ROSE, the Random model Of Sequence Evolution, version 1.3. It simulates the evolution of DNA, RNA, or protein sequences on a randomly generated tree, allowing insertions and deletions and substitution at different rates at different sites as well. It can also use a predefined tree that is input in standard format. It can report ancestral sequences or sequences at the tips of the tree, and it also keeps a record of the true multiple sequence alignment for comparison with the results of multiple sequence alignment programs. ROSE is described in the paper: Stoye, J. D. Evers and F. Meyer. 1998. Rose: generating sequence families. Bioinformatics 14: 157-163. ROSE is available in source code at its web site at http://bibiserv.techfak.uni-bielefeld.de/rose/.

Andy Pang, Andrew Smith, Paulo Nuin and Elisabeth Tillier of the Cancer Genomics and Proteomics Division of the Ontario Cancer Institute and the Department of Medical Biophysics of the University of Toronto, Canada (e.tillier (at) utoronto.ca) have released Simprot (Simulation of Proteins), version 1.03, a program to simulate protein evolution by substitution, insertion and deletion. It allows for several models of amino acid substitution (PAM, JTT and PMB), it allows for gamma distributed sites rates according to Yang's model, and it implements a parameterised Qian and Goldstein distribution model for insertion and deletion. It is described in the paper: Pang, A., A. Smith., P. Nuin, and E. R. M. Tillier. 2005. SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution BMC Bioinformatics 6: 236. It is available as C source code and Windows executables. It can be downloaded from its web site at http://www.uhnresearch.ca/labs/tillier/software.htm

Cory Strope, S. D. Scott and Etsuko Moriyama then of the Department of Computer Science and School of Biological Sciences of the University of Nebraska (corystrope (at) gmail.com) have released indel-Seq-Gen version 2.1.0, a sequence family simulator incorporating domains, motifs, and indels. it simulates a more realistic evolutionary process of protein sequences including insertions and deletions (indels). iSG allows the user to simulate multiple subsequences according to different evolutionary parameters, which is necessary for generating realistic protein families with multiple domains. It tracks all evolutionary events including indels and outputs the "true" multiple alignment of the simulated sequences. iSG can also generate a larger sequence space by allowing the use of multiple related root sequences. It is intended to be used to test the accuracy of multiple alignment methods, phylogenetic methods, evolutionary hypotheses, ancestral protein reconstruction methods, and protein family classification methods. It is described in the paper: Strope, C. L., S. D. Scott, and E. N. Moriyama. 2007. indel-Seq-Gen: A new protein family simulator incorporating domains, motifs, and indels. Molecular Biology and Evolution 24: 640-649. It is available as C source code, Perl script, Linux executables and Intel Mac OS X executables. It can be downloaded from its web site at http://bioinfolab.unl.edu/~cstrope/iSG

  Dmitry Filatov, of the Department of Plant Sciences of the University of Oxford, U.K. (dmitry.filatov  (at) plants.ox.ac.uk) has released ProSeq (Processor of Sequences) version 3. ProSeq is a sequence-editing environment that can do sequence alignment editing, translation, detection of polymorphic sites, and a variety of tests, many of a population-genetic nature, for neutrality and recombination. The part of its capabilities that are relevant to this listing is that it can simulate the evolution of a set of DNA sequences along a coalescent tree, with or without recombination. Version 3 allows simultaneous alignment of multiple loci. An earlier version of ProSeq is described in a paper: Filatov, D.A. 2002. ProSeq: A software for preparation and evolutionary analysis of DNA sequence data sets. Molecular Ecology Notes 2: 621-624. ProSeq is available as Windows or Linux executables from its web site at http://dps.plants.ox.ac.uk/sequencing/proseq.htm.

  Paul Michael Agapow (agapow (at) agapow.net), then of the Department of Biology, Imperial College, Silwood Park, U.K. (most recently of the Health Protection Agency, U.K.) has released MESA (MacroEvolutionary analysis and SimulAtion), version 1.9.23, a program to simulate evolution of a group, allowing for a variety of kinds of extinction mechanisms. It can simulate evolution and describe the diversity of the resulting groups. Its actions can be recorded and repeated on multiple trees. It also has features for editing and manipulating trees. MESA is available as an executable for Windows and as an executable for Mac OS X from its web site at http://www.agapow.net/software/mesa

  Reed Cartwright of the Department of Biology and Biochemistry at the University of Houston, Houston, Texas (reed (at) scit.us) has written DAWG (DNA Assembly With Gaps), version 1.2, a program to simulate evolution of DNA sequences with recombination and gaps. It is designed to simulate the evolution of recombinant DNA sequences in continuous time based on the general time reversible model with gamma and invariant rate heterogeneity and a novel length-dependent model of gap formation. It accepts phylogenies in Newick format and can return the sequence of any node, allowing for the exact evolutionary history to be recorded at the discretion of users. Dawg records the gap history of every lineage to produce the true alignment in the output. Many options are available to allow users to customize their simulations and results. It is described in the paper: Cartwright, R. 2005. DNA Assembly with gaps (DAWG): simulating sequence evolution. Bioinformatics 21 (Supplement 3): iii31-iii38. It is available as C source code. It can be downloaded from its web site at http://scit.us/projects/dawg/wiki

Barry Hall of the Bellingham Research Institute in Bellingham, Washington (barryhall (at) zeninternet.com) has written EvolveAGene3, a program that simulates evolution of a protein sequence along a tree. It generates a bifurcating tree, and assigns branch lengths from a distribution whose mean is specified by the user. A protein sequence is evolved along this tree, with deletions and insertions of codons and with base subtitutions. Substitutions that change the amino acid are accepted with a specified probability. This includes having variable regions of selection intensity, positive or purifying, within the sequence and variation in intensity of selection over branches. Output includes the true tree and unaligned coding sequences and protein sequences as well as the true DNA and the true protein alignments. It is available as Perl script, Windows executables and Mac OS X universal executables. See the web site http://web.me.com/barryghall/Software/Software.html

   Robert Beiko and Robert Charlebois of the Faculty of Computer Science at Dalhousie University (beiko (at) cs.dal.ca) have released EvolSimulator version 2.1.0, a program to simulate the evolution of genes and genomes. EvolSimulator was created to allow the simulation of complex evolutionary regimes, potentially comprising nonstationary and nonuniform processes at the sequence level, alongside genome-level processes such as gene duplication, gene loss, and lateral gene transfer. Several models of LGT are implemented, including random transfers, transfers that favour close relatives in the organismal tree, and preferential transfer among members of the same habitat. It is described in the paper: Beiko, R. G. and R. L. Charlebois. 2007. A simulation test bed for hypotheses of genome evolution. Bioinformatics 23 (7): 825-31. It is available as C++ source code. It can be downloaded from its web site at http://bioinformatics.org.au/evolsim

   Miguel Arenas and David Posada of the Department of Biochemistry, Genetics and Immunology of the University of Vigo, Spain (miguelmmmab (at) gmail.com) have released Recodon (coalescent simulation of Coding sequences with Recombination), version 1.6.0, A simulator of coding sequences based on the coalescent with recombination, migration and demographics. The program simulates coding and non-coding sequences using the coalescent and with recombination, migration and demographics. It implements all major DNA substitution models of evolution and the GY94 codon model including rate heterogenity among codons. It is described in the paper: Arenas, M. and D. Posada, 2007. Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography. BMC Bioinformatics 8: 458. It is available as C source code, Windows executables, Linux executables and Powermac Mac OS X executables. It can be downloaded from its web site at http://darwin.uvigo.es/software/recodon.html

  Miguel Arenas and David Posada of the Department of Biochemistry, Genetics and Immunology of the University of Vigo, Spain (miguelmmmab (at) gmail.com) have released NetRecodon (coalescent simulation with intracodon Recombination), version 6.0.0, A simulator of coding sequences based on the coalescent with (intra and inter codon) recombination, migration and demographics. The program simulates coding and non-coding sequences using the coalescent with recombination (where breakpoints can occur at both intra and inter codon positions), migration and demographics. Indeed, the program implements many DNA substitution models of evolution and also GY94 codon models including heterogenity of rate of evolution among codons. This program is more advanced than the previous program Recodon. One improvement is that it allows recombination within as well as between codons. It is described in the paper: Arenas, M. and D. Posada. 2010. Coalescent simulation of intracodon recombination. Genetics 184(2): 429-437. It is available as C source code, Windows executables, Linux executables and Powermac Mac OS X executables. It can be downloaded from its web site at http://darwin.uvigo.es/software/netrecodon.html

Martin Senger (senger  (at) ebi.ac.uk) of the European Bioinformatics Institute, Hinxton, U.K. and Peter Ernst (P.Ernst  (at) dkfz-heidelberg.de) of the Deutsches Krebsforschungszentrum, Heidelberg, Germany distribute W2H, (Web 2 Husar) version 4.1.2, a web interface for running molecular sequence analysis programs. It can invoke a variety of sequence analysis programs, including the EMBOSS Embassy versions of a number of PHYLIP 3.5 programs. W2H is a set of web pages that has been developed primarily with Unix platforms in mind. They can be downloaded and are available from the W2H web page at http://www.w2h.dkfz-heidelberg.de/

  Juan José de Haro (jjdeharo (at) gmail.com) of "una pequeña ciudad" of the province of Barcelona, Spain, has released Phyledit version 2.0. This is an interactive data editing and analysis program that uses PHYLIP and Treeview for analysis and display of trees. It uses eight programs from PHYLIP, all concerned with discrete 0/1 characters. Phyledit's menus, responses and documentation are all in Spanish. It is a Windows executable downloadable available from its web site at http://perso.wanadoo.es/jjdeharo/phyledit/index.htm. It is available there either by itself or with the PHYLIP and TREEVIEW executables as well.

  Øyvind Hammer, of the Paleontological Museum of the University of Oslo, Norway (ohammer  (at) nhm.uio.no), together with David A.T. Harper of the Geological Museum, Copenhagen, Denmark, and P.D. Ryan, has written PAST (PAleontological STatistics), version 2.04, a package which carries out many kinds of paleontological data analyses, including stratigraphic and morphometric statistics. It also does parsimony analysis, including exhaustive, branch-and-bound and heuristic algorithms for Wagner, Fitch and Dollo parsimony. It does bootstrap methods, strict and majority rule consensus trees, and consistency and retention indices. It calculates three stratigraphic congruency indices with permutation tests. It also does many other statistics and curve fitting. PAST is described in a paper: Hammer, Ø., D.A.T. Harper, and P. D. Ryan. 2001. PAST: Paleontological statistics software package for education and data analysis. Palaeontologia Electronica 4:, issue 1: http://palaeo-electronica.org/2001_1/past/issue1_01.htm. PAST is available from its web site at http://folk.uio.no/ohammer/past/index.html as a Windows executable. Manuals can be read online or downloaded from the web site.

   Matthew Wills of the Department of Biology at the the University of Bath,. U.K. (bssmaw (at) bath.ac.uk) has produced GHOSTS version 2.4, a program for significance tests for RCI, SCI and GER values by randomization. It calculates the Relative Completeness Index (RCI), the Stratigraphic Consistency Index (SCI), and the Gap Excess Ratio (GER) measures of consistency of phylogenies with the stratigraphic record if given one or more tree topologies and stratigraphic range data for up to 74 terminal taxa. It can be used with NEXUS tree files and can be used interactively with MacClade. It can also randomly permute the assignment of stratigraphic ranges among taxa, while holding tree topologies constant, to yield a distribution of values. It tests whether the RCI and SCI values for the original data differ significantly from the random distributions. Its methods are described in the paper: Wills, M. A. 1999. Congruence between phylogeny and stratigraphy: randomization tests. Systematic Biology 48 559-580. It is available as source code for use with Chipmunk Basic. It can be downloaded from the Biodiversity Lab resources web page at http://www.bath.ac.uk/bio-sci/biodiversity-lab/?page_id=281  The program requires a password that can then be obtained from him.

Andrew Rambaut, of the Institute of Evolutionary Biology of the University of Edinburgh, Edinburgh, Scotland (a.rambaut (at) ed.ac.uk) has written QDate version 1.1.1. QDate estimates the date of divergence between two pairs of sequences given that the date of divergence of the members of each pairs is known. It analyzes the data under three models: (1) a perfectly clocklike model, (2) a model in which one pair has a different rate of divergence than the other, and (3) a model in which all branches have different rates. The method is described in the paper: Rambaut, A., and L. Bromham. 1998. Estimating divergence dates from molecular sequences. Molecular Biology and Evolution 15: 442-448. QDate is available from its web page at the IUBIO server at ftp://net.bio.net/iubionew/molbio/evolution/phylo/QDate/main.html. It is available as C source code for Unix or as a Macintosh or Windows executable.

Marc Robinson-Rechavi, of the Department of Ecology and Evolution of the Université de Lausanne, Lausanne, Switzerland (Marc.Robinson-Rechavi  (at) unil.ch) has written RRTree, (Relative Rate tests within a Tree), version 1.1. It carries out relative rate tests for equality of evolutionary rates in DNA or protein sequences between lineages, taking into account the structure of the tree, which can be input in a number of common formats. In addition sequences are read in. The methods are described in a papers:

• Robinson, M., M. Gouy, C. Gautier, and D. Mouchiroud. 1998. Sensitivity of the relative-rate test to taxonomic sampling, Molecular Biology and Evolution 15: 1091-1098.
• Robinson-Rechavi, M. and D. Huchon. 2000. RRTree: Relative-rate tests between groups of sequences on a phylogenetic tree. Bioinformatics 16: 296-297.

Bette Korber of the Theoretical Division, Los Alamos National Laboratory , Los Alamos, New Mexico (btk  (at) lanl.gov), Mark Muldoon and and their colleagues have released programs for rate evolution which implement the method described by Jeff Thorne, Hirohisa Kishino, and Ian Painter of North Carolina State University for making a maximum likelihood estimate of the phylogeny while allowing rates of evolution to change along the tree in a "relaxed molecular clock". Their method was described in a paper: Thorne, J. L., H. Kishino, and I. S. Painter. 1998. Estimating the rate of evolution of the rate of molecular evolution. Molecular Biology and Evolution 15: 1647-1657. Korber and her colleagues used it for their paper: Korber, B., M. Muldoon, J. Theiler, F. Gao, R. Gupta, A. Lapedes, B. H. Hahn, S. Wolinksy and T. Bhattacharya. 2000. Timing the ancestor of the HIV-1 pandemic strains. Science 288: 1789-1796. Three programs are available (all as C code for Unix):

• mlcov, which produces a covariance matrix (Hessian matrix) of rates among branches which is needed by the other programs,
• rate-evolution, which carries out the method of Thorne et. al. and gives likelihoods and estimates of rates on the different branches (a version which was used in the Science paper is available as well as a corrected version written by Muldoon), and
• TREEPAINT, which takes a Postscript file from the tree-drawing program TreeTool and "colorizes" it by classifying branches into five categories by their estimated rates of evolution.

Jeff Thorne of the Department of Genetics at North Carolina State University, Raleigh, North Carolina (thorne (at) statgen.ncsu.edu) has written Multidivtime, version 09.25.03, a program that estimates divergence times from multiple-locus data. The method starts with a given tree supplied by the user. The Bayesian dating method implemented in multidivtime uses a probabilistic model to describe the change in evolutionary rate over time and uses a Markov chain Monte Carlo (MCMC) procedure to derive the posterior distribution of rates and times. It allows simultaneous use of different substitution models for multiple data partitions as well as multiple calibration windows, and provides direct credibility intervals for estimated divergence times and substitution rates. The dating method is described in an earlier paper: Thorne, J. L., H. Kishino, and I. S. Painter. 1998. Estimating the rate of evolution of the rate of molecular evolution. Molecular Biology and Evolution 15: 1647-1657. It is available as C source code which can be compiled on Mac OS X or other standard Unix systems, and as Windows executables. Multidivtime is to be used in combination with some of the programs from Ziheng Yang's PAML package. Multidivtime can be downloaded from its web site at http://statgen.ncsu.edu/thorne/multidivtime.html. An earlier version is available from Ziheng Yang's lab at their web site at http://abacus.gene.ucl.ac.uk/software.html where it is called T3, the Thornian Time Traveler. Yang suggests using the more recent version at Thorne's site.

Tae-Kun Seo of the Professional Programme for Agricultural Bioinformatics of the University of Tokyo, Japan (seo (at) iu.a.u-tokyo.ac.jp) has written CodonRates version 1.0, a program to estimate divergence times and absolute rates of synonymous and nonsynonymous substitution with protein-coding genes. Given sequences and a tree, CodonRates can separate the amount of evolution into time and the synonymous and nonsynonymous rates without using a molecular clock. Data other than sequences, such as fossil constraints and a prior distribution for the root time, are required. It is described in the paper: Seo T-K, H. Kishino, and J. L. Thorne. 2004. Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences. Molecular Biology and Evolution 21(7): 1201-1213. It is available as C++ source code and Windows executables. It can be downloaded from its web site at http://www.iu.a.u-tokyo.ac.jp/~seo/software.htm

Tom Britton, Cajsa Anderson, David Jacquet, Samuel Lundqvist, and Kåre Bremer of the Department of Mathematics and the Department of Systematic Botany of Stockholm University, Stockholm, Sweden (Anderson is at Uppsala Univerity) (tomb (at) math.su.se) have released PATHd8 (Path-date), a program to estimate divergence times from a nonclocklike tree and time constraints. PATHd8 reads in a tree which has branch lengths but with no requirement that these show a molecular clock. It also reads in constraints on the divergence times. These are then reconciled using either the PATHd8 method or the Mean Path Length method. It is described in the papers:

• Britton, T. 2005. Estimating divergence times in phylogenetic trees without a molecular clock. Systematic Biology 54 (3): 500-507.
• Britton, T., B. Oxelman, A. Vinnersten, and K. Bremer. 2002. Phylogenetic dating with confidence intervals using mean path lengths. Molecular Phylogenetics and Evolution 24: 58-65.

Bette Korber of the Theoretical Division, Los Alamos National Laboratory , Los Alamos, New Mexico (btk  (at) t10.lanl.gov), and her colleagues have released BRANCHLENGTH, a pair of programs which allow trees to have their branch lengths to any node plotted against time. They take output files from the PHYLIP program DNAML, or from Gary Olsen's program fastDNAmlM, or from one of the modified versions of fastDNAml as input. One program (BRANCHLENGTHxTIME) plots branch lengths to any specified node against time, makes best fit lines, and does Monte Carlo resampling statistics. The other program (BRANCHLENGTH) computes The sum of branch lengths to any specified node. Korber and her colleagues used it for their paper: Korber, B., M. Muldoon, J. Theiler, F. Gao, R. Gupta, A. Lapedes, B. H. Hahn, S. Wolinksy and T. Bhattacharya. 2000. Timing the ancestor of the HIV-1 pandemic strains. Science 288: 1789-1796. The programs are available from the web site for the programs from that paper at http://www.santafe.edu/~btk/science-paper/bette.html. Some further code (scripts and C code) to fully implement the methods used for branch length plotting in that paper is available from Korber on request to individuals who have the book Numerical Recipes and thus have a license to use code derived from it.

Kai Müller of the Institute for Evolution and Biodiversity of the Westfälische Wilhelms-Universität Münster, Münster, Germany (kaimueller (at) uni-munster.de) has written GRate (Group relative RATE tests), version 1.0, a program for carrying out relative rate tests of evolution in specified groups. GRate runs PAUP* and uses the sitewise log likelihoods and bootstrapping that it makes available, and analyzes these to carry out relative rate tests that compare the rate of evolution in two or more clades selected by the user. It is available as Windows executables. It can be downloaded from its web site at http://bioinfweb.info/Software/GRate

Nicolas Galtier and Manolo Gouy of the Institut des Sciences de l' Evolution of the Université Montpellier 2 - CNRS, Montpellier, France and the Laboratoire de Biométrie et Biologie Evolutive of the Universiteacute; Claude Bernard - Lyon, France (galtier (at) univ-montp2.fr) have produced NHML (NonHomogenous Maximum Likelihood), version 3, a maximum likelihood phylogeny program using a nonhomogenous model of nucleotide change. It uses a model developed by them which is not reversible and thus allows information about the location of the root of the tree. The program can evaluate a user-defined tree, or can start with a "star tree" and then resolve it by Subtree Pruning and Regrafting rearrangements to infer the phylogeny. It can use either a model of rates varying among sites or covarion-like model which allows rates at each site to independently vary along the branches of the tree. The methods are described in the papers:

• Galtier N. and M. Gouy. 1998. Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. Molecular Biology Evolution 15: 871-879.
• Galtier N., N. Tourasse N. and M. Gouy. 1999. A nonhyperthermophilic common ancestor to extant life forms. Science 283: 220-221.
• Galtier N. 2001. Maximum-likelihood phylogenetic analysis under a covarion-like model. Molecular Biology and Evolution 18: 866-873.

Mike Maciukenas, then at the Department of Microbiology of the University of Illinois, wrote a wonderful X-windows based interactive tree-plotting program called TreeTool, version 2.02. It takes as input a PHYLIP tree file, with branch lengths if they are provided, displays the tree in either rooted or unrooted form on any X-windows screen, and allows the user to modify the form of the tree and the placement of nodes and labels. When the tree is in final form the user can have it written to a Postscript or PICT file and/or printed to a Postscript-compatible printer. TreeTool is free as a C program for X windows using the Xview library. Xview seems to be available mostly on Sun workstations (it can also be installed on Linux). TreeTool is available It will be found in the IUBIO software archive at http://iubio.bio.indiana.edu/soft/molbio/unix/treetool. It is also included in the GDE sequence analysis environment mentioned. A Debian Linux Treetool package for Intel-compatible processors is available at its Debian web page at http://packages.debian.org/lenny/treetool. It has links to the Debian package for Xview.

     Rod Page of the Division of Environmental and Evolutionary Biology of the University of Glasgow, Scotland (r.page  (at) bio.gla.ac.uk), has written TreeView version 1.6.6, a program for displaying and manipulating trees. It can draw rooted and unrooted trees, display bootstrap values, and edit trees by moving branches, collapsing them, and rerooting. The program reads NEXUS, PHYLIP, and Hennig86 style tree files (including files produced by fastDNAml and CLUSTALW), and can save trees in the same formats so that it can convert trees among these formats. The Mac and Windows versions have almost identical interfaces. They can support the standard fonts available on Macs and PCs, and they support the standard PICT and Windows Metafile formats for output, allowing tree pictures to be copied into other applications, as well as being saved in files. There is a print preview and drag-and-drop facilities. Currently TreeView can read trees with up to 1000 taxa. The program is free, and can be obtained from its web page from http://taxonomy.zoology.gla.ac.uk/rod/treeview.html. It comes in Mac OS and Windows executable versions. There is also a Unix/Linux version, TreeView X, which does not yet implement all features of the program. Source code is available at its page at Google Code at http://code.google.com/p/treeviewx/its page at Google Code. There is also online help including an online manual.

  Manolo Gouy of the Laboratoire de Biomètrie et Biologie Evolutive of the University of Lyon, France (mgouy  (at) biomserv.univ-lyon1.fr), has produced NJplot, version 2.3-2, which plots rooted phylogenies (input in the standard form) and saves the plots as Postscript (for Mac OS, PICT) files. It displays branch lengths and bootstrap information (if present) and allows the user to swap branches and change the position of the root. It is described in the paper Perrière, G. and M. Gouy 1996. WWW-Query: an on-line retrieval system for biological sequence banks. Biochimie 78: 364-369. It is available free as executables for Mac OS X, Mac OS, Windows, SunOS, Sun Solaris, Linux and DEC/Compaq/HP Alpha. It can be retrieved using its web page at http://pbil.univ-lyon1.fr/software/njplot.html. A Debian Linux package is available from its web page at http://packages.debian.org/unstable/science/njplot. It has links to a number of other Debian packages that are needed to run it, including Lesstif and the NCBI Vibrant toolkit. It is also available in a server at the Institut Pasteur in Paris.

  Manolo Gouy of the Laboratoire de Biomètrie et Biologie Evolutive of the University of Lyon, France (mgouy  (at) biomserv.univ-lyon1.fr), has written unrooted, which draws unrooted phylogenies and saves them in Postscript files (for Macintosh, PICT files). It is available free as executables for Mac OS X, Mac OS, Windows, SunOS, Sun Solaris, SGI, IBM Unix, Linux and DEC/Compaq/HP Alpha. It can be retrieved using its web page at http://pbil.univ-lyon1.fr/software/unrooted.html.

  Tadashi Imanishi (imanishi  (at) jbirc.aist.go.jp) of the Biological Information Research Center (BIRC) of the National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan has produced DendroMaker, version 4.1, Mac OS programs which can draw trees on the screen and print them in Postscript files or MacPaint files. They read the trees in from tree files produced by the Neighbor-Joining or UPGMA options of the Oden package, and can also read standard Newick-format tree files. They can them edit them and reroot them in a variety of ways. They can produce PICT files of the trees. DendroMaker is distributed as Mac OS PowerMac or 68k Mac executables (each available in both English and Japanese versions) from its web page at http://www.cib.nig.ac.jp/dda/timanish/dendromaker/home.html.

  Don Gilbert (gilbertd  (at) bio.indiana.edu) of the Department of Biology of the University of Indiana, Bloomington, Indiana, has written Tree Draw Deck, a Hypercard deck that draws trees on the screen from standard Newick-format tree files. The deck, which runs on Macintoshes or PowerMacs that have Hypercard Player, is based on two programs, Drawtree and Drawgram, from the 3.3 version of PHYLIP. It allows mouse-driven interactive display of the trees with selection of options for display, and allows the resulting plot to to cut into the system clipboard and pasted into drawing programs such as MacDraw or Canvas. Its printing and file-saving options do not at present work, but the clipboard method works. It is available by anonymous ftp from ftp.bio.indiana.edu in directory molbio/mac. It is also available by ftp from ftp.ebi.ac.uk in directory pub/software/mac.

  Don Gilbert (gilbertd  (at) bio.indiana.edu) of the Department of Biology of the University of Indiana, Bloomington, Indiana, has written Phylodendron version 0.8d beta, a Java application for drawing phylogenetic trees. It will read tree data in standard Newick format, then display graphical views of the phylogenetic tree. Various options allow you to modify, adorn and edit the tree. Standard application functions to save, print, edit and manage preferences are included. This program will not estimate nor produce the tree data. Phylodendron is written as a Java application. It is also distributed with some extra parts for Mac OS. Phylodendron is an enhancement of the Mac Hypercard program Tree Draw Deck which was released by Gilbert in 1990, and uses tree drawing algorithms from PHYLIP. Phylodendron is available from its Web site http://iubio.bio.indiana.edu/soft/molbio/java/apps/trees/ or by anonymous ftp from iubio.bio.indiana.edu in directory molbio/java/apps/trees/. Source code is also available there. Phylodendron is also made available as a web server.

Julian Gough (gough  (at) cs.bris.ac.uk) of the Department of Computer Science at the University of Bristol, Bristol, U.K. has produced a Phylogenetic Tree Drawing Perl module that reads a tree and displays a rooted tree diagram. The user can specify width of the diagram and its line thickness, and can make each line consist of two shadings of different width, and add extra labels to tips. The routine is in Perl and is available at its web site at http://www.cs.bris.ac.uk/~gough/software/. Selecting the "Perl module" link there displays the Perl source on the browser, and you can then save it to disk. It is also available at his previous web site for it at http://supfam.mrc-lmb.cam.ac.uk/treedraw/tree.html

  Tamara Munzer (tmm  (at) cs.ubc.ca) and her colleagues at the Graphics, Visualization and Human-Compuyer-Interface group at the Department of Computer Science of the University of British Columbia, Vancouver, Canada have produced TreeJuxtaposer version 2.1. This displays a tree or shows two trees, with the locations of differences highlighted. Parts of the trees collapse and expand as one moves through the trees, so that very large trees can be examined. TreeJuxtaposer is a Java application which works with GL4Java, the Java implementation of the OpenGL graphics environment. TreeJuxtaposer is described in a paper for the SIGGRAPH 2003 conference: Munzner, T., F. Guimbretiere, S. Tasiran, L. Zhang, and Y. Zhou. 2003. TreeJuxtaposer: Scalable tree comparison using focus+context with guaranteed visibility. ACM Transactions on Graphics 22: 453-462. It was an overall winner in the IEEE Symposium on Information Visualization InfoVis 2003 Contest on "Visualization and Pair Wise Comparison of Trees". It can be downloaded from its web site at http://olduvai.sourceforge.net/tj/index.shtml

Christian Zmasek, currently of the Genomics Institute of the Novartis Research Foundation in San Diego, California (phylosoft  (at) gmail.com) has written Archaeopteryx, version 0.971β9m, a software tool for the visualization, analysis, and editing of potentially large and highly annotated phylogenetic trees. It is the successor to ATV, a tree viewer that is part of the FORESTER package. Archaeopteryx can read trees from a variety of tree file formats. It can do a number of different shapes of tree display, can have support values on the tree, allows different colors and display of various kinds of data such as photographs of the organisms. It can also display internal node data by mouse rollover as you move the mouse around the tree. Archaeopteryx is written in Java, and can be run on Sun Java version 5 and later. That version of Java is already installed in recent Windows and Mac OS X systems, and can also be installed by the user on Linux systems. Archaeopteryx is available at its web site at http://www.phylosoft.org/archaeopteryx/. There are also available there versions that can also be installed as an applet on Java-enabled browsers.

  Richard H. Ree of the Botany Department of the Field Museum of Natural History, Chicago, Illinois (rree  (at) fieldmuseum.org) has written Mavric (recursively, MAvric Visualizes RIck's Cladograms), version 0.8.3, a package in the Python language for the manipulation and visualization of phylogenetic data. It is intended to be flexible and easily customizable to suit the needs of phylogenetic biologists who use python. Mavric is named for its core application Mavric, which aims to provide a graphical interface to phylogenies in a manner similar to MacClade. (Rick notes that “the recursion that defines the name Mavric ultimately boils down to its central application: a tool to Manipulate And Visualize RIck's Cladograms -- if you followed all this you're pretty far ahead in understanding recursion”). Currently, its main usefulness is to view and manipulate phylogenetic trees. Branches can be moved around, pruned, rotated, have lengths changed. Trees can be grafted together, and viewed either rooted or unrooted. Postscript tree plots can be produced. Mavric is available as Python source code from its web site at http://www.bioinformatics.org/mavric/index.html.

  Andrew Rambaut, of the Institute of Evolutionary Biology of the University of Edinburgh, Edinburgh, Scotland (a.rambaut (at) ed.ac.uk) and Mike Charleston (mcharles  (at) it.usyd.edu.au) of the Sydney University Biological Informatics and Technology Centre, Sydney, Australia have produced the TreeEdit Phylogenetic Tree Editor version 1.0a10. TreeEdit is an application for organizing, manipulating and viewing sets of trees. It is intended as a tool for preparing sets of trees for use in phylogeny packages. It can read and write trees in standard formats (PHYLIP, NEXUS, and CAIC). It allows drag-and-drop editing of branches, cut and paste of trees between windows (as NEXUS text), rerooting by clicking on branches, editing species labels, rotating branch order at polytomies, including and excluding species, and transforming branch lengths (including Sanderson's non-parametric rates smoothing) and many other interactive features. TreeEdit is available as an executable for Mac OS 8 or later at its web site at http://tree.bio.ed.ac.uk/software/treeedit/

  Andrew Rambaut, of the Institute of Evolutionary Biology of the University of Edinburgh, Edinburgh, Scotland (a.rambaut (at) ed.ac.uk) wrote TreeThief version 1.0, a program for inputting phylogenetic trees, with branch lengths, into the computer for use in other programs. The tree is input by clicking on each node in turn. A scanned image of a tree can be loaded first to act as a template. TreeThief is distributed from its web page at http://microbe.bio.indiana.edu:7131/soft/iubionew/molbio/evolution/phylo/TreeThief/ as a Mac OS executable. It requires a Macintosh running Mac OS 8 or later.

Thomas Laubach and Arndt von Haeseler of the Bioinformatics Institute of the University of Duesseldorf, Germany (thomas.laubach (at) uni-duesseldorf.de) and the Center of Integrative BioInformatics Vienna at the University of Vienna, Austria (arndt.von.haeseler (at) univie.ac.at) have produced TreeSnatcher Plus, a program to capture phylogenies from images. TreeSnatcher Plus is a GUI-driven Java program for the semi-automatic recognition of multifurcating phylogenetic trees in pixel images. The program accepts an image file as input and analyzes the topology and the metrics of a tree depicted, with user assistance. The analysis is carried out in a multiple-stage process using basic algorithms from the field of image analysis. It yields a tree in the standard Newick format that represents the tree structure, optionally including branch lengths. TreeSnatcher Plus can process trees with more than 100 leaves or more in a few seconds. It also allows the user to construct their own trees and to modify existing trees. An earlier version, Treesnatcher 1.0, is described in the paper: Laubach, T. and A. von Haeseler. 2007. TreeSnatcher: Coding trees from images. Bioinformatics 23: 3384-3385. It is available as Java executables, packaged for Windows, for Linux, and for Mac OS X. Its web site is available at two locations, at the University of Düsseldorf at http://www.cs.uni-duesseldorf.de/AG/BI/Software/treesnatcher/ and at the University of Vienna at http://www.cibiv.at/software/treesnatcher/. The same versions are available at both sites.

Koichiro Tamura of the Evolutionary Genetics Laboratory, Tokyo Metropolitan University, Tokyo, Japan (koichiro-tamura  (at) c.metro-u.ac.jp) has written TreeExplorer version 2.12, a program for plotting, rearranging, and editing trees, including a feature to compress a subtree to make essential features more visible. TreeExplorer is intended to work with MEGA but can also be used to read and edit or view trees in other standard formats. It is distributed as a Windows executable from its web site at http://evolgen.biol.metro-u.ac.jp/TE/TE_man.html where a manual for the program and a download link will be found.

A (large) group headed by Katherine St. John at Lehman College, City University of New York (stjohn (at) lehman.cuny.edu), David Hillis and Tandy Warnow of the University of Texas, Austin (DHillis (at) mail.utexas.edu and tandy (at) cs.utexas.edu), and including numerous other people, has released Tree Set Viz, a program in Java for visualizing distances between sets of trees in a space. It computes distances between trees and uses these to infer points in a two-dimensional space that most closely approximate those distances. It is to be used in the Mesquite Java project for interacting with trees. Tree Set Viz is described in a paper: Hillis, D. M., T. A. Heath, and K. St. John. 2005. Analysis and visualization of tree space. Systematic Biology 54: 471-482. It is available from its web site at http://comet.lehman.cuny.edu/treeviz/software.html

  Dominik Hepperle of Sequentix, Dorfstrasse 20, D-18249 Klein Raden, Germany (info (at) do-mix.de) has released TreeMe, a program for visualisation and annotation of phylogenies. It can read and write trees, allows many kinds of annotation of nodes, rearrangement and editing of the tree, addition of multiple bootstrap values, collapsing of nodes, and more. It is available as a Windows executable from its web site in the company web sites at http://science.sequentix.de/software_treeme.php. It is purchased for 499 Euros for the first license, 199 Euros for each additional license, and 149 Euros for upgrade licenses.

   Jörn Müller, of Pipinstraße 2, Bonn, Germany, Ben Stöver of the Nees-Institut für Biodiversität der Pflanzen, Rheinische Friedrich-Wilhelms-Universität Bonn, Germany (stoever (at) bioinfweb.info) and Kai Müller, of the group on Evolution and Biodiversity of Plants at Westfälische Wilhelms-Universität Münster, Germany (kaimueller (at) uni-muenster.de) have written TreeGraph 2 (version 2.0.45-197 beta), an editor for phylogenetic trees. It allows automatically combining information from different phylogenetic analyses and helps to identify and graphically present incongruencies. It features editing and formatting options, such as automatically setting line widths or colors according to the value of any of the unlimited number of variables that can be assigned to each node or branch. These node/branch data can be imported from spread sheets or other trees, be calculated from each other, be kept invisible or set visible and then be freely formatted. Whole clades can be copied from other files and be inserted, and can also be manually added. It can read NEXUS or Newick tree files, or its own TGF format, which uses a LaTeX-style format that is like those formats, but extended to indicate support values for nodes as well as annotations for groups of tips or clades. The program produces EPS, SVG, PDF or PNG graphics file formats. It is described in the papers:

• Stöver, B. C., and K. F. Müller. 2010. TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses. BMC Bioinformatics 11: 7.
• Müller, J. and K. Müller. 2004. TreeGraph: automated drawing of complex tree figures using an extensible tree description format. Molecular Ecology Notes 4: 786-788.

   Adrian Canutescu and Roland Dunbrack of the Basic Science Division at the Fox Chase Cancer Center (Roland.Dunbrack (at) fccc.edu) have released ArboDraw version 1.0, a Windows program for creating, rendering, coloring, annotating, and saving images of phylogenetic trees. ArboDraw (from Latin, arbor, tree) is a Windows program for creating publication-quality images of phylogenetic trees. ArboDraw provides a combination of features:

1. editing of the rendered tree, including independent horizontal and vertical scaling, full font control, and background and tree coloring;
2. branch selection and coloring so that separate parts of the tree can be colored differently;
3. annotation of sequences from the input FASTA header lines available on mouseover; labels and annotations can be edited as desired;
4. control of saving the image in png format at desired resolution for publication;
5. saving of the image in a novel XML format so that editing can be re-started from a previous editing session;
6. running a fast and accurate sequence alignment program, MUSCLE, for generating trees; A MUSCLE executable is included with ArboDraw.
7. alternatively allowing user input tree data in Newick format.

François Chevenet and colleagues, of the Laboratoire de Génétique et Evolution des Maladies Infectieuses of the Institut de recherche pour le développement, UMR CNRS/IRD 2724, Montpellier, France (f.chevenet (at) ird.fr) have written TreeDyn version 198.3, modules for dynamic graphics and annotation of trees. TreeDyn can import trees, and place annotations on their nodes, branches, and clades. It can compare trees and find parts of trees which are similar to a highlighted region on a target tree. Operations in TreDyn can be scripted. It can handle very large trees and can collapse regions on those trees to concentrate on certain parts of the tree. TreDyn can handle multiple windows and multiple trees per window, can save and restore graphical analysis, can project texts or symbols facing leaf labels or linked to nodes. It includes a library of packages dedicated to specific research fields involving trees. It is described in the paper: Chevenet, F., C. Brun, A. L. Banuls, B. Jacq and R. Christen. 2006. TreeDyn: towards dynamic graphics and annotations for analyses of trees. BMC Bioinformatics 7: 439. It is available as source code in the graphics-oriented scripting language Tcl/Tk. There are separate distributions for Windows, for Linux, and for Mac OS X, for systems that already have Tcl/Tk installed. It can be downloaded from its web site at http://www.treedyn.org/

Robin Kramer, then of the Digital Biology Laboratory, Computer Science Department of the University of Missouri, Columbia, Missouri (whose email address was at that time: kramer (at) mizzou.edu) has produced DigTree (Digital Tree). DigTree is a tool that allows biologist to display large heirarchical trees in ways that preserve weights such as branch lengths. It can also display other sorts of trees. It is described in the paper: Kramer, R., V. Olman, Y. Xu, and D. Xu. 2006. DigitalTree: A tool for displaying biological data in tree structure. Lecture Notes in Computer Science vol. 3992, pp. 855-862. It is available as C++ source code and Windows executables. To compile it, one also needs the spirit++ framework in addition to a C++ compiler. TreeDyn can be downloaded from its web site at http://digbio.missouri.edu/~digtree/

Olivier Elemento, then of the LIRMM (Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier) at the Université de Monpellier II, Montpellier, France and now of the Institute for Computational Biomedicine at Weill Cornell Medical College, New York Citys (ole2001 (at) med.cornell.edu), has released DTdraw (Duplication Tree Draw), a program to draw trees of gene duplication histories. a command line tool to draw tandem duplication histories. Tandem duplication trees can be reconstructed with the DTscore program. DTdraw takes as input a (rooted) duplication history in Newick format, and an order file, i.e. a file which contains the number of leaves and the leaf labels of the tree, in correct order. At the moment, DTdraw outputs drawings in two graphical formats : PNG and Postscript. It is available as C source code and Linux executables. It can be downloaded from its web site at http://www.lirmm.fr/~elemento/DTdraw/

   Paul Michael Agapow, of the Department of Biology of Imperial College at Silwood Park, Ascot, Berks U.K. (agapow (at) agapow.net) has written TreeMaker, version 1.3, a program for interactive construction of taxonomies with species richness data. It allows the user to create a taxonomy and write out a tree that has species richness information on it. It is described in the paper: Crozier, R. H., L. J. Dunnett, P.-M. Agapow. 2005. Phylogenetic biodiversity assessment based on systematic nomenclature. Evolutionary Bioinformatics Online 1: 11-36. It is available as C source code, Windows executables and Mac OS X executables. It can be downloaded from its web site at http://www.agapow.net/software/treemaker. (TreeMaker is not related to this program of the same name)

Mike Sanderson of the Department of Ecology and Evolutionary Biology at the University of Arizona, Tucson, Arizona (sanderm (at) email.arizona.edu) has written Paloverde version 1.1, a program to display a phylogeny in one of several 3-dimensional formats. Paloverde is best used for trees of 100 to 2,500 tips. It reads the tree from a NEXUS tree file and can display it in a number of ways. These include a circular format, on a spiral, a cone, a hemisphere or in a three-dimensional treelike form. The user can rotate the object and zoom on it, and clades can be selected to be plotted. Subclades can also be collapsed to single tips. It is available as C source code and Powermac Mac OS X executables. It can also be compiled from the source code on Linux systems. It requires the free OpenGL graphics library. It can be downloaded from its web site at http://loco.biosci.arizona.edu/paloverde/paloverde.html

  Alessandro Zuccon and Dario Zuccon of the Department of Vertebrate Zoology at the Naturhistoriska riksmuseet, Stockholm, Sweden have produced MrEnt, version 2.2, a program to produce drawings of phylogenies. It is intended for drawing high-quality, printable phylogenetic trees. It is intended as a user-friendly program to recognize Nexus tree files and display them in the most commonly used tree formats. Trees can be displayed as rectangular cladograms, slanted cladograms or phylograms. The program allows full editing of taxon names, taxon comments, support values, and branches, addition of other graphic elements such as lines, shapes, text, brackets). Drawings can be exported in Portable document format (PDF), Windows enhanced metafile (EMF), Windows bitmap (BMP), or Portable Network Graphics (PNG) formats. It also allows multiple trees, layers and embedded graphics. It is available as a Windows executable. It also requires that the Microsoft .NET framework be installed. It can be downloaded from its web site at http://www.mrent.org"

  Andrew Rambaut of the Institute of Evolutionary Biology of the University of Edinburgh, Edinburgh, Scotland (a.rambaut (at) ed.ac.uk) has produced FigTree version 1.3.1, a program to graphically view phylogenies and prepare publication-ready figures from them. FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. Andrew notes that it was written for his own needs so may not be as polished and feature-complete as a commercial program. In particular it is designed to display summarized and annotated trees produced by BEAST. It is available as Java executables and Windows executables. It is available from its web site at http://tree.bio.ed.ac.uk/software/figtree/

  Jonathan Bingham, then of Sugen, Inc. (more recently at Jivan Biologics: jbingham (at) jivanbio.com) wrote HyperTree version 12, a phylogenetic tree viewer, with a hyperbolic ('fish-eye') view and editing abilities that help in managing very large trees. HyperTree includes many features for navigating large trees, such as the ability to visualize large trees with hundreds of nodes or more, to rotate and drag the display in cartesian space, to search and select nodes, to copy clusters for pasting into other programs, to color-code branches, to zoom in and out, and to label branches (eg, common family members). It can view phylogenetic trees and other hierarchical clusterings, such as gene expression profile clusters. The program subsequently came to be owned by Pfizer, Inc., which has given permission to the Salk Institute for its distribution at the kinase.com web site. It is described in the paper: Bingham, J. and S. Sudarsanam. 2000. Visualizing large hierarchical clusters in hyperbolic space Bioinformatics 16(7): 660-661. It is available as Java executables. It can be downloaded from its web site at http://kinase.com/tools/HyperTree.html

  Daniel Huson, with contributions from Tobias Dezulian, Markus Franz, Christian Rausch, Daniel Richter and Regula Rupp of the Center for Bioinformatics of the Tuebingen University, Tuebingen, Germany (huson (at) informatik.uni-tuebingen.de) has released Dendroscope 2, an interactive program for the visualization and navigation of phylogenetic trees. Dendroscope is a new program for the interactive visualization and navigation of phylogenetic trees. The program provides eight standard tree visualizations and is optimized to handle trees containing hundreds of thousands of taxa. The program allows trees to be edited as well as for graphics to be exported. Version 2 adds the capability of displaying networks as well as trees. To support the inspection of large trees, Dendroscope offers a magnification tool. It is written in Java and and installers are provided for Linux/Unix, MacOS X and Windows. It is described in the paper: Huson, D. H., T. Dezulian, M. Franz, C. Rausch, D. C. Richter and R. Rupp. 2007. Dendroscope: an interactive viewer for large phylogenetic trees, submitted for publication. Dendroscope can be downloaded from its web site at http://www-ab.informatik.uni-tuebingen.de/software/dendroscope for free, although the authors require that you obtain a free license key online and cite their paper in any publication using the program.

Gregory Jordan of the Goldman Group of the European Bioinformatics Institute (phylowidget (at) gmail.com) or greg (at) ebi.ac.uk) has written PhyloWidget version 1.0, a web-friendly tool for creating, editing, and visualizing trees. PhyloWidget is a phylogenetic tree visualization program that "plays nice" with the Internet. It runs directly from the browser window (as a Java applet), and trees can be loaded in manually from the user's hard drive, or alternatively through a URL-based API. They can be displayed and edited, and publication-quality figures produced. PhyloWidget is aimed at (1) users who want a simple, easy-to-use tree visualization tool without having to download software, and (2) phylogenetic tree databases who wish to use the URL API to let PhyloWidget visualize the database's trees. It is described in the paper: Jordan, G. E. and W. P. Piel. 2008. PhyloWidget: Web-based visualizations for the tree of life. Bioinformatics 24: 1641-1642. It is available as Java source code and Java executables, and a browser-based Java applet. It can be downloaded from its web site at http://www.phylowidget.org/

John Brzustowski of the Department of Biological Sciences of the University of Alberta, Edmonton, Canada (jbrzusto (at) ualberta.ca) has written TreeToy , a program to view a tree and select subtrees from it. TreeToy reads a tree from a file and displays it. The user can reroot the tree or select subtrees to write out. It can also be zoomed and written out in a PICT2 format for printing. It is available as Java source code and Java executables. It can be downloaded from its web site at http://www2.biology.ualberta.ca/jbrzusto/TreeToy.php

   Stephen A. Smith and Casey W. Dunn, of the Department of Ecology and Evolutionary Biology of Brown University, Providence, Rhode Island (stephen_a_smith (at) brown.edu) have produced Phyutility version 2.2, a utility to modify trees and to perform certain data set modifications as well. Phyutility's tree operations include rerooting, pruning, type conversion, consensus trees, measures of leaf stability, of the varying attachment locations of lineages, and measures of tree support. It can also do some data operations such as concatenating alignments, parsing Genbank files, trimming alignments, and searching for and fetching sequences from the Genbank database. It is described in the paper: Smith, S. A. and C. W. Dunn. 2008. Phyutility: a phyloinformatics tool for trees, alignments, and molecular data. Bioinformatics 24: 715-716. It is available as Java source code and Java executables. It needs two additional Java libraries downloadable from elsewhere. It can be downloaded from its web site at http://code.google.com/p/phyutility/

Catherine Anderson of the Department of Computer Science of the University of Nebraska, Lincoln (cateander27 (at) gmail.com) has released SuiteMSA (A suite of tools for visual comparision of Multiple Sequence Alignments), version 1.3.14, Contains tools that allow the visual and quantitative comparison between multiple sequence alignments using sequence sets as well as structural information. . This package contains tools that allow the visual and quantitative comparison between MSA using sequence sets as well as structural information. Various color scheme are available including color schemes based on structural information. The Pixel Plot tool allows the display of multiple large alignment in a pixelated display that gives the overall shape of the alignments as well as column wise comparison. Included in this package is a sequence simulator, iSGv2. It can also act as a GUI and call the alignment programs ClustalW and MUSCLE, and it also has as a phylogeny display. It is described in the paper: Anderson, C. L., C. L. Strope and E. N. Moriyama. 2011. SuiteMSA: Visual tools for multiple sequence alignment comparison and molecular sequence simulation. BMC Bioinformatics 12: 184. It is available as Perl script, Java executables and Intel Mac OS X executables. It can be downloaded from its web site at http://bioinfolab.unl.edu/~canderson/SuiteMSA/

David Kidd and Xianhau Liu of the National Evolutionary Synthesis Center at Duke University, Durham, North Carolina (dk (at) nescent.org) have released GeoPhyloBuilder version 1.0.2, an extension for the widely-used geographic information system program ArcGIS that creates geophylogenies. Geophylogenies are spatial networks in which network topology is defined by a phylogenetic model and the geographical position of nodes and branch paths are derived from a biogeographical model. Tree depths are assigned to the z-dimension of the spatial network facilitating rapid 3D visualization in GIS or other software. Geophylogenies can be output in ArcGeodatabase, shapefile and KML (Google Earth) format. A copy of ArcGIS is required. GeoPhyloBuilder is described in the paper: Kidd, D. M. and X. Liu. 2007. geophylobuilder 1.0: an ArcGIS extension for creating 'geophylogenies'. Molecular Ecology Notes 8 (1): 88-91. It is available as Windows executables and source code for the Microsoft C++ .NET compiler. It can be downloaded from its web site at http://www.nescent.org/informatics/software.php

   Donovan Parks and Robert Beiko of the Faculty of Computer Science at Dalhousie University, Halifax, Nova Scotia, Canada (beiko (at) cs.dal.ca) have released GenGIS version 1.08, a Geospatial Information System for Genetic Data. GenGIS allows the integration of digital map data alongside information about sequences and sample locations. A wide range of data visualizations are supported, and phylogenetic trees or cluster relationships can be drawn in two or three dimensions. A Python interface provides extensibility and camera controls, while the R statistical package allows exposed data to be subjected to statistical analysis. It is described in the paper: Parks, D. H., M. Porter, S. Churcher, S. Wang, C. Blouin, J. Whalley, S. Brooks, and R. G. Beiko. 2009. GenGIS: A geospatial information system for genetic data. Genome Research 19: 1896-1904. It is available as C++ source code, Windows executables and Mac OS X universal executables. It can be downloaded from its web site at http://kiwi.cs.dal.ca/GenGIS/Main_Page

Richard H. Ree and Stephen A. Smith of the Department of Botany of the Field Museum of Natural History (rree (at) fieldmuseum.org) has released Lagrange (Likelihood analysis of geographic range evolution), version 2.0.1, likelihood models for geographic range evolution on phylogenetic trees, with methods for inferring rates of dispersal and local extinction and ancestral ranges. Lagrange (likelihood analysis of geographic range evolution) is a freely available Python package, co-authored by Ree and Smith, implementing dispersal-extinction-cladogenesis models of geographic range evolution, methods described in papers by Ree et al. (Evolution, 2005) and Ree and Smith, 2008. It can be used to infer geographic ancestry (historical ranges) and estimate rates of dispersal and local extinction on phylogenetic trees that have species range data arrayed at their tips. A web server that is an analysis configuration tool that prepares files to be run on your copy of Lagtange is available at: http://www.reelab.net/lagrange. Lagrange is described in the paper: Ree, R. H. and S. A. Smith. 2008. Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Systematic Biology 57(1): 4-14. It is available as C++ source code and Python script. It can be downloaded from its web site at http://code.google.com/p/lagrange/

  Campbell Webb, David Ackerley, and Steven Kembel of the Arnold Arboretum of Harvard University, of the University of California, Berkeley, and the Center for Ecology and Evolutionary Biology of the University of Oregon (cwebb (at) oeb.harvard.edu) have written Phylocom (software for the analysis of PHYLOgenetic COMmunity structure and character evolution) version 4.1, a program to measure phylogenetic community structure and carry out comparative methods analysys. It can measure community phylogenetic structure (Webb's mean phylogenetic distance, mean nearest phylogenetic neighbour distance, NRI and NTI, Faith's phylogenetic diversity, phylogenetic distances among samples and taxa) and compare observed patterns to those expected under various null models of community assembly and phylogeny structure. It cna also carry out comparative methods for the analysis of character evolution and speciation (independent contrasts, lineages through time, and trait evolution under different evolutionary models). In addition it can manipulate phylogenetic trees and ecological community data (converting Newick to Nexus format, pruning and merging phylogenetic trees, and doing data randomization using one of several null models). It can turn species lists into phylogenies with branch lengths based on fossil age estimates. It is available as C++ source code, Windows executables and Mac OS X universal executables. It can be downloaded from its web site at http://www.phylodiversity.net/phylocom/

Gabriel Valente and Rod Page of the Department of Software of the Technical University of Catalonia, Barcelona, Spain and the Division of Environmental and Evolutionary Biology of the Institute of Biomedical and Life Sciences at the University of Glasgow, Scotland (valiente (at) lsi.upc.edu) have produced Forest version 0.1, programs for producing or using edit scripts to convert one tree to another in the GML graph representation language. GML, the Graph Modelling Language (not to be confused with the Geographic Markup Language GML) is a file format for graphs. Forest contains programs to take two trees written in GML format, and produce an edit script that can convert one into the other. It also contains a program to apply the script to a tree. It is described in the paper: Page, R. D. M. and G. Valiente. 2005. An edit script for taxonomic classifications. BMC Bioinformatics 6: 208. It is available as C++ source code. i To compile this the user also needs to have the Graph Template Library. Forest can be downloaded from its web site at http://darwin.zoology.gla.ac.uk/~rpage/forest/

  Steven Brewer (sbrewer  (at) bio.umass.edu) of the Biology Department, University of Massachusetts, Amherst, Massachusetts, and Robert Hafner, formerly of Western Michigan University have developed Phylogenetic Investigator version 2.01, a teaching program that allows students to connect together organisms from a data set provided to them, to make phylogenies and examine them. The program is a Mac OS executable. Phylogenetic Investigator and its manual are downloadable here at http://bioquest.org/BQLibrary/library_details.php?product_id=22909. It is described in two papers:

• Brewer, S.D. 1996. A problem-solving Approach to the teaching of evolution. Bioscene 22: 11-17.
• Brewer, S.D. 1996. Towards improved teaching of evolution: The co-evolution of Phylogenetic Investigator and a conceptual/procedural knowledge base. BioQUEST Notes 6(3): 11-17.

David Joyce, of the Department of Mathematics and Computer Science, Clark University, Worcester, Massachusetts (djoyce  (at) clarku.edu) makes available the Phylap program, version 0.2, a Java applet that teaches about inferring phylogenies from molecular sequences using some clustering algorithms. The program allows the user to choose some parameters including the number of species, the rate of evolution and how many states there are at sites in the molecule. The program then chooses a random tree and evolves sequences on it, then computes distances between the sequences and infers the tree by one of several clustering methods. The user can see the results at each stage. The java applet may be downloaded from its web site at http://babbage.clarku.edu/~djoyce/java/Phyltree/cover.html, and if your browser can run Java programs it can of course also run the applet when browsing that page.

  I (Joe Felsenstein, Department of Genome Sciences and Department of Biology, University of Washington, Seattle, joe  (at) gs.washington.edu) have written a program, Dnatree version 1.3, for teaching about molecular phylogenies. The program uses a crude character-mode (not GUI) user interface. It is based on several programs from PHYLIP. The user chooses some rate parameters and the number of species. The program then simulates a random tree using a birth process and displays it. The user can then have the program simulate evolution of a stretch of DNA sequence along this tree. Then the program displays a different random tree, showing the number of changes inferred along that tree by a parsimony criterion. It allows the user to manually rearrange the tree to try to minimize the number of changes. Dnatree is available as C source code and as executables for Linux, Windows, and Mac OS X from its web site at http://evolution.gs.washington.edu/dnatree/dnatree.html Some executables of an earlier version, 1.1, are also available there for Mac OS, 68k Macintoshes, SunOS, Compaq/Digital Alpha, and IBM AIX.

Dave Dobson of the Geology Department of Guilford College, Greensboro, North Carolina (ddobson (at) guilford.edu) has written SimpleClade, a program that allows simple cladistic analysis with a graphical user interface. SimpleClade takes a data file in a common spreadsheet format, with values in the columns which are treated as identifiers of discrete states. It displays an arbitrary tree and then allows you to manually rearrange it interactively. The parsimony score is displayed as you do so. Outgroups can be chosen and the directions of the state changes are displayed as well as the tree. The program was written primarily as a teaching tool. It is available as a Windows executable. It can be downloaded from its web site at http://www2.guilford.edu/geology/simpleclade/

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