Cymon J. Cox (Research Associate)
cymon@duke.edu

Education:

B.Sc. University of Wales (UCNW, Bangor) U.K. 1994
Ph.D. University of Reading U.K. 1998

Biography:

Born England. Spent many years in Brighton, Sussex, then passed through North Wales, Edinburgh, Reading, and London, before arriving in Durham NC.

Research:

Systematics, phylogenetics, diversity, and diversification of mosses and fungi. Read the papers :)
Python, Zope, PostGreSQL, RedHat/Fedora Core, and a few pieces of software...

Publications:

Phylogenetic relationships among the ciliate arthrodontous mosses: evidence from chloroplast and nuclear DNA sequences.
Cox, C.J. & Hedderson T.A. 1999. Plant Systematics and Evolution, 215: 119-139. Abstract

Bryophytes and the origins and diversification of land plants: new evidence from molecules.
Hedderson, T.A.,Chapman R.L., & Cox C.J.. 1998. In Ashton N.W., J.W. Bates, & J.G. Duckett (Eds.), Bryology for twenty-first century. Maney, Leeds. Pp. 65-78. Publisher

Phylogenetic relationships of the Wardiaceae (Musci): evidence from 18s rRNA and rps4 gene sequences.
Hedderson, T.A., Cox C.J., & Gibbings G. 1999. The Bryologist, 102: 26-31.

Phylogenetic relationships among the diplolepideous-alternate mosses (Bryidae) inferred from nuclear and chloroplast DNA sequences.
Cox, C.J., Goffinet B., Newton A.E., Shaw A.J., & Hedderson T.A.J. 2000. The Bryologist, 103(2): 224-241.

Evolution of the major moss lineages: Phylogenetic analyses based on multiple gene sequences and morphology.
Newton, A.E., Cox C.J., Duckett J.G., WheelerJ., Goffinet B., Hedderson T.A.J., & Mishler B. D. 2000. The Bryologist, 103(2): 187-211.

Phylogenetic relationships among the basal-most diplolepideous mosses with special emphasis on the evolutionary significance of the Funariineae.
Goffinet, B. & Cox C.J., 2000. The Bryologist, 103(2): 212-213.

The Bryophyta (Mosses): Systematic and evolutionary inferences from the rps4 gene (cpDNA) phylogeny.
Goffinet, B., Cox C.J., Shaw A.J., & Hedderson T.A.J. 2001. Annals of Botany, 87: 191-208.

Phylogeny and molecular evolution of the Amblystegiaceae (Bryopsida).
Vanderpoorten, A., Hedenäs L., Cox C.J. &, Shaw A.J. 2002. Molecluar Phylogenetics and Evolution, 23: 1-21.

Circumscription, classification, and taxonomy of the Amblystegiaceae (Bryopsida) inferred from nuclear and chloroplast DNA sequence data and morphology.
Vanderpoorten, A., Hedenäs L., Cox C.J. &, Shaw A.J. 2002. Taxon, 51: 115-122.

Phylogenetic and biosystematic relationships in four highly disjunct polyploid complexes in the subgenera Ceterach and Phyllitis in Asplenium (Aspleniaceae).
Pinter, I., Bakker, F., Barrett, J., Cox, C., Gibby, M., Henderson, S., Morgan-Richards, M., Rumsey, F., Russell, S., Trewick, S., Schneider, H., & Vogel, J. 2002. Organisms, Diversity & Evolution, 2(4): 299-311. Abstract

A new species of Leskeodon (Daltoniaceae) from Ecuador.
Buck, W. R., Shaw A.J. & Cox C.J.. 2002. Brittonia, 54: 178-180.

Phylogenetic relationships within the moss family Bryaceae based on chloroplast DNA evidence.
Cox, C.J.& Hedderson T.A.J. 2003. Journal of Bryology, 25: 31-40.

Global patterns in peatmoss biodiversity.
Shaw, A.J., Cox C.J., & Boles S.B. 2003. Molecular Ecology, 12: 2553-2570.

Phylogenetic evidence of a rapid radiation of pleurocarpous mosses (Bryophyta).
Shaw, A.J., Cox C.J., Goffinet B., Buck W.R., & Boles S.B. 2003. Evolution, 57(10): 2226-2241.

A taxonomic reassessment of the Vittiaceae (Hypnales, Bryopsida): evidence from phylogenetic analyses of combined chloroplast and nuclear sequence data.
Vanderpoorten, A., Goffinet B., Hedenäs L., Cox C.J., & Shaw A.J. 2003. Plant Systematics and Evolution, 241: 1-12. Abstract

Evolution of multiple paralogous adenosine kinase gene in the moss genus Hygroamblystegium: Phylogenetic implication.
Vanderpoorten, A., Shaw, A.J., & Cox, C.J. 2004. Molecular Phylogenetics and Evolution, 31: 505-516.

Phylogenetic relationships of Haplolepideous mosses (Dicranidae) inferred from rps4 gene sequences.
Hedderson, T.A., Murray, D.J., Cox, C.J., & Nowell, T.L. 2004. Systematic Botany, 29(1): 29-41.

Ordinal relationships of pleurocarpous mosses, with special emphasis on the Hookeriales.
Buck, W.R., Cox, C.J., Shaw, A.J., & Goffinet, B. (In press.) Systematics and Biodiversity, (Botany).

Phylogenetic relationships among Sphagnum sections, Hemitheca, Isocladus, and Subsecunda.
Shaw, A.J., Cox, C.J., & Boles, S.B. 2004. The Bryologist, 107(2) 189-196.

Phylogeny of the Bryaceae inferred from morphological and molecular evidence.
Pedersen N., Cox, C.J., & Hedenäs, L. 2003. Systematic Botany, 28: 471-482.

Diversification of peatmosses: a phylogenetic approach.
Shaw, A.J., Cox, C.J., & Melosik, I. 4004. In Molecular Systematics of Bryophytes, pp. 340-254. [Eds.] B. Goffinet, V. Hollowell, & R. Magill. Missouri Botanical Garden Press, Missouri.

Phylogenetic inferences in the dung-moss family Splachnaceae from analyses of cpDNA sequence data and implications for the evolution of entomophily.
Goffinet, B., Shaw, A.J., & Cox, C.J. 2004. American Journal of Botany, 91(5): 748-759.

Phylogeny and evolution of medical species of Candida and related taxa: A multigenic analysis.
Diezmann, S., Cox, C.J., Vilgalys, R., Mitchell, T.G. & Schoenian, G. 2004. Journal of Clinical Microbiology, 42(12): 5624-5635.

Phylogenetic Relationships among the Mosses Based on Heterogeneous Bayesian Analysis of Multiple Genes from Multiple Genomic Compartments.
Cox, C.J., Goffinet, B., Shaw, A.J., & Boles, S.B. 2004. Systematic Botany, 29(2): 234-250.

Phylogeny, species delimitation, and recombination in Sphagnum section Acutifolia.
Shaw, A.J., & Cox, C.J., & Boles, S.B. 2005. Systematic Botany, 30(1): 16-33.

Chloroplast phylogeny of Asplenioid ferns based on rbcL and trnL-F spacer sequences (Polypodiidae, Aspeleniaceae) and its implications for biogeography.
Schneider, H., Russell, S.J., Cox, C.J., Bakker, F., Henderson, S., Rumsey, F., Barrett, J., Gibby, M., & Vogel, J. 2004. Systematic Botany, 29(2): 260-274.

Phylogenetic inferences in the Orthotrichoideae (Orthotricaceae: Bryophyta) based on variation in four loci from all genomes.
Goffinet, B., Shaw, A.J., Cox, C.J., Wickett, N.R., & Boles, S.B. 2004. In Molecular Systematics of Bryophytes, pp. 270-289. [Eds.] B. Goffinet, V. Hollowell, & R. Magill. Missouri Botanical Garden Press, Missouri.

Where are we in assembling the fungal tree of life, classifying the fungi, and understanding the evolution of their subcellular traits?
François Lutzoni, Frank Kauff, Cymon J. Cox, David McLaughlin, Gail Celio, Bryn Dentinger, Mahajabeen Padamsee, David Hibbett, Tim James, Elisabeth Baloch, Martin Grube, Valérie Reeb, Valérie Hofstetter, Conrad Schoch, A. Elizabeth Arnold, Jolanta Miadlikowska, Joseph Spatafora, Desiree Johnson, Sarah Hambleton, Michael Crockett, Robert Shoemaker, Gi-Ho Sung, Robert Lücking, Thorsten Lumbsch, Kerry O'Donnell, Manfred Binder, Paul Diederich, Damien Ertz, Cécile Gueidan, Benjamin Hall, Karen Hansen, Richard C. Harris, Kentaro Hosaka, Young-Woon Lim, Yjauan Liu, Brandon Matheny, Hiromi Nishida, Don Pfister, Jack Rogers, Amy Rossman, Imke Schmitt, Harrie Sipman, Jeffrey Stone, Junta Sugiyama, Rebecca Yahr, & Rytas Vilgalys. 2004. American Journal of Botany, 91:1446-1480.

Global patterns of moss diversity: taxonomic and molecular inferences.
Shaw, A.J., Cox, C.J., & Goffinet, B. 2005. Taxon 54(2): XXX-XXX

Software

TCT - Tree Congruence Tester -- a P4 extension module or command line executable

$ ./tct.py -h
usage: tct.py [options] treefile1 treefile2
 
Tree Congruence Test(er): reads two rooted trees (NEXUS and/or PHYLIP format),
reciprocally prunes each tree of missing taxa (automatic), deletes any taxa
passed to the programme (via -d), and tests topological congruence among the
remaining clades supported by a value greater than the set threshold.
 
Version 1.5 Aug 25 2004
Cymon J. Cox & Frank Kauff cymon@duke.edu, fkauff@duke.edu
 
options:
  -h, --help            show this help message and exit
  -tTHRESHOLD, --threshold=THRESHOLD
                        Support threshold. (Default = 0.95)
  -rROOT_TAXON, --root-with=ROOT_TAXON
                        Specify taxon to root trees. NB: If you misspell the
                        taxon name the programme will exit abruptly. (Optional
                        if input trees already rooted to the same taxon)
  -dDELETE, --delete-taxa=DELETE
                        Taxa specified in a file will be deleted from the
                        congruence test. The input file should be a plain ASCII
                        text file with one taxon on each line, as they appear in
                        the tree description, and without punctuation. Use this
                        to iterate over taxon deletion until no conflicts occur.
                        (Optional)
  -oOUTFILE, --outfile-name=OUTFILE
                        Write results to named file. (Default is to write to
                        standard out)
  -w, --write-tree-files
                        Write the pruned trees used for the tree congruence test
                        in (alt)NEXUS format. File names are the tree name from
                        the input NEXUS tree file + TCT(1 or 2).nex. A NEXUS
                        sets block containing a taxset of taxa deleted from the
                        tree is included in a comment in the written tree file.
                        (Default is to not write the trees)
  -p, --write-eps-files
                        Write an EPS picture file of the tree. The tree has
                        nodes labelled with the node numbers attached to help
                        identify clades in the conflict descriptions (this
                        requires a modified version of p4). NB: Currently
                        printing of the EPS file is incorrect but the file is
                        viewable. (Default is to not write EPS pictures)
  -v, --verbose         If set, all taxa in a clade are printed. (Default output
                        prints only the first and last three taxa of a clade in
                        conflict)

Matrix Melder - Combining Nexus Formatted Alignment Matrices

Command line execution: 

usage: matrix-melder [options] matrix1 matrix2
 
Matrix Melder: Combine Nexus and/or SeAl formatted files into a single
interleaved Nexus file with missing entries for the relevent partitions.
 
Version  1.5 Fri Mar 18 2005
Cymon J. Cox 
 
options:
  -h, --help            show this help message and exit
  -c, --commandline-execution
                        Execute command line without the GUI
  -l, --write-log       Write a log file
  -oOUTFILE, --outfile-name=OUTFILE
                        Write results to named file. (Default is to write to a
                        file named 'meldedMatrix.nex')

Installation:

$ tar zxvf matrix-melder-1.5.tar.gz
matrix-melder-1.5/
matrix-melder-1.5/matrix-melder.glade
matrix-melder-1.5/setup.pyc
matrix-melder-1.5/matrix-melder-icon.png
matrix-melder-1.5/PKG-INFO
matrix-melder-1.5/setup.pyo
matrix-melder-1.5/setup.py
matrix-melder-1.5/matrix-melder.desktop
matrix-melder-1.5/MANIFEST.in
matrix-melder-1.5/matrix-melder
matrix-melder-1.5/matrix-melder.gladep
matrix-melder-1.5/README
$ cd matrix-melder-1.5
 As an administrator...
$ sudo python setup.py install
running install
running build
running build_scripts
creating build/scripts-2.3
copying and adjusting matrix-melder -> build/scripts-2.3
changing mode of build/scripts-2.3/matrix-melder from 644 to 755
running install_scripts
copying build/scripts-2.3/matrix-melder -> /usr/bin
changing mode of /usr/bin/matrix-melder to 755
running install_data
copying matrix-melder.glade -> /usr/lib/matrix-melder
copying matrix-melder.desktop -> /usr/share/applications
copying matrix-melder-icon.png -> /usr/share/pixmaps
$ matrix-melder -h
usage: matrix-melder [options] matrix1 matrix2
 
Matrix Melder: Combine Nexus and/or SeAl formatted files into a single
interleaved Nexus file with missing entries for the relevent partitions.
 
Version  1.5 Fri Mar 18 2005
Cymon J. Cox 
 
options:
  -h, --help            show this help message and exit
  -c, --commandline-execution
                        Execute command line without the GUI
  -l, --write-log       Write a log file
  -oOUTFILE, --outfile-name=OUTFILE
                        Write results to named file. (Default is to write to a
                        file named 'meldedMatrix.nex')

WritePartitions.py -- a P4 extension module or command line executable
(Another common task that annoys me every time I do it...)

$ WritePartitions.py -h
 
usage: WritePartitions.py [options] infile
 
Writes a separate Nexus or Phylip formatted file for each sub-partition
defined within a character partition of a Nexus formatted alignment.
 
Version 0.1 Fri Apr 22 2005
Cymon J. Cox cymon@duke.edu
 
options:
  -h, --help            show this help message and exit
  -pPART, --parition_name=PART
                        Name of the character partition who's subsets are to
                        be written to files
  -fFORMAT, --format=FORMAT
                        Output format (Nexus or Phylip) default Nexus
  -eEXCLUDE, --exclude_charset=EXCLUDE
                        Character sets to be excluded
  -lNAME_LENGTH, --length=NAME_LENGTH
                        Taxon name length for Phylip
                        files(default: 10 - max 40) WARNING - not currently
                        supported by official p4 release.

PD.py -- a P4 extension module to conduct Phylogenetic Diversity (PD - sensu Faith, 1992) analyses

p4> help(PD.calculatePDofClade)
calculatePDofClade(theTree, theNode, verbose=False)
    Calulate PD (phyloenetic diversity) of a clade
     
    theTree - p4.Tree instance
    theNode - int node number
    verbose - draw() and dump() clade of interest
     
    Return: float -> pd of clade
      
p4> help(PD.writePDPAUPFile)
writePDPAUPFile(fName, theTree, clades, treeFileName=None, includeTaxaBlock=True, writeLogFile=True, quoteTaxonNames=False)
    Write a Nexus formatted paup file for phylogenetic diversity analyses (PD - Faith, 1992)
     
    fName               - output file name
    theTree             - a p4.Tree instance
    treeFileName        - if not None, write a nexus tree file that paup will use to calculate PD
                            else theTree.fName will be tree used to calculate PD
    clades              - dict of {cladeName:[taxon1, taxon2], cladeName2:[taxon1, taxon2], etc...}
                            taxon1 and taxon2 are 2 taxa one each from the two sibling clades derived from the root node
                            of the clade in interest
    includeTaxaBlock    - write a nexus taxa block (default True)
    writeLogFile        - have Paup write a log file when executing the PD analysis (default True)
    quoteTaxonNames     - quote the taxon label if they contain an underscore (default False)
     
    Return: -> void

Diversity Simulations - bunch of standalone Python scripts to wrap Phylogen, Genie, and Diversi, performing the analyses described in Phylogenetic evidence of a rapid radiation of pleurocarpous mosses (Bryophyta)

    Includes:
  • Multi_Div_Simul_Analysis_wrap.py -- wrapper around Simulation_analyses_wrapper.py
  • Simulation_analyses_wrapper.py 
    $ Simulation_analyses_wrapper.py -h
usage: Simulation_analyses_wrapper.py [options]
 
options:
  -h, --help            show this help message and exit
  -bBIRTH, --birthrate=BIRTH
                        Phylogen Birth rate (default=0.2)
  -dDEATH, --deathrate=DEATH
                        Phylogen Death rate (default=0.1)
  -eEXTANT, --extanttaxa=EXTANT
                        Number of extant taxa in simulated trees
  -sSAMPLE, --samplesize from the simulated trees=SAMPLE
                        Number of taxa to sample from the simulated trees
  -fRUN_FILE_NAME, --runname=RUN_FILE_NAME
                        The name prefix for this analysis (e.g. 'run1')
  -rREPLICATES, --numberofreplicates=REPLICATES
                        The number of Phylogen replicates i.e. the number of
                        trees to generate
  • Genie_generator.py -- generate LTT plots using Genie 
    $ Genie_generator.py -h
usage: Genie_generator.py [options]
 
options:
  -h, --help            show this help message and exit
  -tTN, --treenumber=TN
                        Number of trees
  -fFILENAME, --file=FILENAME
                        Tree file name
  -oOUTFILENAME, --oufile=OUTFILENAME
                        Name of file to write output (optional will default to
                        genis.sh)
  -gLOGFILENAME, --logfilename=LOGFILENAME
                        Name of the log file for genie to output
  • Genie_ltt_parser.py -- Parse LTT plots from Genie 
    $ Genie_ltt_parser.py -h
usage: Genie_ltt_parser.py [options]
 
options:
  -h, --help            show this help message and exit
  -nN, --numberoftaxa=N
                        Number of taxa in trees
  -tT, --numberoftrees=T
                        Number of trees
  -oOUTFILENAME, --outfile=OUTFILENAME
                        Name of file to write lineage through time summary
                        output (optional will default to ltts.out)
  -iINFILENAME, --infile=INFILENAME
                        Name of the file to parse
  -dFLAG, --diversi=FLAG
                        Write diversi format trees (0 (default) = NO 1 = YES)
  -lFLAG2, --ltt=FLAG2  Write ltt summary data (0 = NO 1 (default) = YES)
  -pDIVERSI_FILE_PREFIX, --diversifileprefix=DIVERSI_FILE_PREFIX
                        Prefix to use when writing Diversi files. X.div will be
                        added to the prefix, where X is the tree number
  • Diversi_Generator.py -- Generate Diversi input files 
    $ Diversi_Generator.py -h
usage: Diversi_Generator.py [options]
 
options:
  -h, --help            show this help message and exit
  -tNUMBER_OF_TREES, --treenumber=NUMBER_OF_TREES
                        Number of trees
  -fDIVERSI_SHELL_NAME, --shellfilename=DIVERSI_SHELL_NAME
                        Diversi shell file name
  -oDIVERSI_RESULT_FILE_NAME, --diversiresultfilename=DIVERSI_RESULT_FILE_NAME
                        Name of log file to write Diversi results
  -pDIVERSI_FILE_PREFIX, --diversifileprefix=DIVERSI_FILE_PREFIX
                        Diversi file name prefix (diversi_file_prefix + '_' +
                        str(y) + '.div')
  -vTC_VALUE, --diversiTCvalue=TC_VALUE
                        Diversi TC value (default = 50)
  • Diversi_out_parser.py -- Parse Diversi output files 
    $ Diversi_out_parser.py -h
usage: Diversi_out_parser.py [options]
 
options:
  -h, --help            show this help message and exit
  -fFILE, --infile=FILE
                        read input from FILE
  -oOUTFILE, --outfile=OUTFILE
                        write output to OUTFILE
  -cFLAG, --multipleCs=FLAG
                        Set to 1 to run multiple C models
  -bBETA_FILENAME, --betasFileName=BETA_FILENAME
                        Name of the file to write the Model B beta values
                        (Default: Diversi_betas.out)
usage: Diversi_out_parser.py [options]

IMPORTANT - these scripts are very alpha quality and may or may not work. It is highly recommended that you have a working knowledge of the Python programming langauge and that you check the code and results very carefully. Be scared... be very scared! May 2004

Fedora Core 2 RPM packages of various phylogenetics software...

MrModeltest - mrmodeltest-2.2-1.i386.rpm - mrmodeltest-2.2-1.src.rpm (Updated: Tue 22 Feb 2005)
Modeltest - modeltest-3.7-1.i386.rpm - modeltest-3.7-1.src.rpm (Updated: Wed 22 Jun 2005)
Phyml - phyml-2.4.4-1.i386.rpm - phyml-2.4.4-1.src.rpm (Updated: Tue 22 Feb 2005)
MrAIC.pl - mraic.pl-1.4-1.i386.rpm - mraic.pl-1.4-1.src.rpm (Updated: Mon 28 Mar 2005)
Mark Pagels BayesPhylogenies - BayesPhylogenies-1-1.i386.rpm - BayesPhylogenies-1-1.src.rpm
Sequin - sequin-5.35-1.i386.rpm - sequin-5.35-1.src.rpm
SeaView - seaview-0.0-3.i386.rpm - seaview-0.0-3.src.rpm
Consel - consel-0.1-h.i386.rpm - consel-0.1-h.src.rpm (Updated: Tue 22 Feb 2005)
Phyl-O-Gen - phylogen-1.1-1.i386.rpm - phylogen-1.1-1.src.rpm
Seq-Gen - Seq-Gen-1.3.2-1.i386.rpm - Seq-Gen-1.3.2-1.src.rpm (Updated: Tue 22 Feb 2005)

OpenOffice Bibliography - biblio.dbf (almost exclusively moss and phylogenetics references)