Bioinformatics Tools for the Multilocus Phylogenetic Analysis of Fungi

  • Devarajan ThangaduraiEmail author
  • Jeyabalan Sangeetha
Part of the Fungal Biology book series (FUNGBIO)


Mycologists are generally identifying fungal communities by microscopic and macroscopic assessment. This conventional approach has several limitations due to the growth and environmental factors. Hence, molecular techniques and bioinformatics tools are essential in the field identification and characterization of fungi. Multilocus sequences are widely used in most of the bioinformatics tools and they can be used to recognize species boundaries. Nucleic acid and protein sequences-based analysis in fungal studies are revolutionizing the view on mycology. Numerous bioinformatics tools are available online to guide molecular biologists and biotechnologists. This chapter provides a guide to utilizing the available bioinformatics tools on the World Wide Web for sequence alignment, editing, and multilocus phylogenetic analysis.


Bioinformatics Tools Softwares Databases Multilocus phylogenetic analysis Fungi 


  1. 1.
    Kolbert CP, Persing DH (1999) Ribosomal DNA sequencing as a tool for identification of bacterial pathogens. Curr Opin Microbiol 2:299–305PubMedCrossRefGoogle Scholar
  2. 2.
    Abd-Elsalam KA (2003) Bioinformatics tools and guideline for PCR primer design. Afr J Biotechnol 2:91–95Google Scholar
  3. 3.
    Yan PV (2005) Bioinformatics: new research. Nova Science Publishers, New YorkGoogle Scholar
  4. 4.
    Pevsner J (2009) Bioinformatics and functional genomics. John Wiley & Sons, New York, pp 1–13CrossRefGoogle Scholar
  5. 5.
    Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60PubMedCrossRefGoogle Scholar
  6. 6.
    Gardes M, Bruns T (1993) ITS primers with enhanced specificity for Basidiomycetes—application to the identification of mycorrhizae and rusts. Mol Ecol 2:113–118PubMedCrossRefGoogle Scholar
  7. 7.
    Seifert KA (2009) Progress towards DNA barcoding of fungi. Mol Ecol Resour 9:83–89PubMedCrossRefGoogle Scholar
  8. 8.
    Muller GM, Bills GF, Foster MS (2004) Biodiversity of fungi: inventory and monitoring methods. Elsevier Academic, San Diego, CA, 341Google Scholar
  9. 9.
    Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM, Margulies EH et al (2003) Comparative analyses of multi-species sequences from targeted genomic regions. Nature 424:788–793PubMedCrossRefGoogle Scholar
  10. 10.
    Tripathi KK (2000) Bioinformatics: the foundation of present and future biotechnology. Curr Sci 79:570–575Google Scholar
  11. 11.
    Jones NC, Zhi D, Raphael BJ (2006) AliWABA: alignment on the web through an A-Bruijn approach. Nucleic Acids Res 34:613–616CrossRefGoogle Scholar
  12. 12.
    Raphael B, Zhi S, Tang H, Pevzner P (2004) A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Res 14:2336–2346PubMedCrossRefGoogle Scholar
  13. 13.
    Schwartz S, Zhang Z, Frazer KA, Smit A, Riemer C, Bouk J et al (2000) PipMaker—a web server for aligning two genomic DNA sequences. Genome Res 10:577–586PubMedCrossRefGoogle Scholar
  14. 14.
    Baxevanis AD, Ouellette BFF (2001) Bioinformatics: a practical guide to the analysis of genes and proteins. John Wiley & Sons, Inc., New YorkGoogle Scholar
  15. 15.
    Schwartz A, Pachter L (2006) Multiple alignment by sequencing annealing. Bioinformatics 23:24–29CrossRefGoogle Scholar
  16. 16.
    Madden T (2005) The BLAST sequence analysis tool. In: McEntyre J, Ostell J (eds) NCBI handbook. National Library of Medicine, Bethesda, M. DGoogle Scholar
  17. 17.
    Parry-Smith DJ, Payne AWR, Michie AD, Attwood TK (1997) CINEMA—a novel colour interactive editor for multiple alignments. Gene 211: GC45–GC56Google Scholar
  18. 18.
    Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H et al (2007) clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948PubMedCrossRefGoogle Scholar
  19. 19.
    Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG et al (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31:3497–3500PubMedCrossRefGoogle Scholar
  20. 20.
    Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680PubMedCrossRefGoogle Scholar
  21. 21.
    Crottini A, Dordel J, Köhler J, Glaw F, Schmitz A, Vences M (2009) A multilocus phylogeny of Malagasy scincid lizards elucidates the relationships of the fossorial genera Androngo and Cryptoscincus. Mol Phylogenet Evol 53:345–350PubMedCrossRefGoogle Scholar
  22. 22.
    Ye SQ (2008) Bioinformatics: a practical approach. Chapman & Hall/CRC Press, Boca Raton, FLGoogle Scholar
  23. 23.
    Qi J, Luo H, Hao B (2004) CVTree: a phylogenetic tree reconstruction tool based on whole genomes. Nucleic Acids Res 32:W45–W47PubMedCrossRefGoogle Scholar
  24. 24.
    Stoye J (1997) Divide-and-Conquer multiple sequence alignment. Dissertation thesis, Universitat Bielefeld, Bielefeld, GermanyGoogle Scholar
  25. 25.
    Stoye J, Perrey SW, Dress AWM (1997) Improving the Divide-and-Conquer approach to sum-of-pairs multiple sequence alignment. Appl Math Lett 10:67–73CrossRefGoogle Scholar
  26. 26.
    Brinkmann A, Dress AMW, Perrey SW, Stoye J (1997) Two applications of the divide & conquer principle in the molecular sciences. Math Program 79:71–97Google Scholar
  27. 27.
    Stoye J, Moulton V, Dress AWM (1997) DCA: an efficient implementation of the Divide-and-Conquer multiple sequence alignment algorithm. CABIOS 13:625–626PubMedGoogle Scholar
  28. 28.
    Stoye J (1998) Multiple sequence alignment with the Divide-and-Conquer method. Gene 211:GC45–GC56PubMedCrossRefGoogle Scholar
  29. 29.
    Chikkagoudar S, Roshan U, Livesay DR (2007) eProbalign: generation and manipulation of multiple sequence alignments using partition function posterior probabilities. Nucleic Acids Res 35:W675–W677PubMedCrossRefGoogle Scholar
  30. 30.
    Gouet P, Courcelle E, Stuart DI, Metoz F (1999) ESPript: multiple sequence alignments in PostScript. Bioinformatics 15:305–308PubMedCrossRefGoogle Scholar
  31. 31.
    Jaroszewski L, Li Z, Cai XH, Weber C, Godzik A (2011) FFAS server: novel features and applications. Nucleic Acids Res 39:W38–W44PubMedCrossRefGoogle Scholar
  32. 32.
    Jaroszewski L, Rychlewski L, Li Z, Li W, Godzik A (2005) FFAS03: a server for profile-profile sequence alignments. Nucleic Acids Res 33:W284–W288PubMedCrossRefGoogle Scholar
  33. 33.
    Torarinsson E, Havgaard JH, Gorodkin J (2007) Multiple structural alignment and clustering of RNA sequences. Bioinformatics 23:926–932PubMedCrossRefGoogle Scholar
  34. 34.
    Havgaard JH, Lyngsø RB, Gorodkin J (2005) The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search. Nucleic Acids Res 33:W650–W653PubMedCrossRefGoogle Scholar
  35. 35.
    Nikhat Z, Mazumder R, Seto D (2001) Comparisons of gene co-linearity in genomes using GeneOrder2.0. Trends Biochem Sci 26:514–516CrossRefGoogle Scholar
  36. 36.
    Mazumder R, Kolaskar A, Seto D (2001) GeneOrder compares the order of genes in small genomes. Bioinformatics 17:162–166PubMedCrossRefGoogle Scholar
  37. 37.
    Chalmel F, Lardenois A, Thompson JD, Muller J, Sahel JA, Léveillard T et al (2005) GOAnno: GO annotation based on multiple alignment. Bioinformatics 21:2095–2096PubMedCrossRefGoogle Scholar
  38. 38.
    Brodie R, Roper RL, Upton C (2004) JDotter: a Java interface to multiple dotplots generated by dotter. Bioinformatics 20:279–281PubMedCrossRefGoogle Scholar
  39. 39.
    Huang X, Miller W (1991) The lalign program implements the algorithm of Huang and Miller. Adv Appl Math 12:337–357CrossRefGoogle Scholar
  40. 40.
    Barker D (2004) LVB: parsimony and simulated annealing in the search for phylogenetic trees. Bioinformatics 20:274–275PubMedCrossRefGoogle Scholar
  41. 41.
    Toh K (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 9:286–298PubMedCrossRefGoogle Scholar
  42. 42.
    Toh K (2010) Parallelization of the MAFFT multiple sequence alignment program. Bioinformatics 26: 1899–1900PubMedCrossRefGoogle Scholar
  43. 43.
    Zhu H, Schein CH, Braun W (2000) MASIA: recognition of common patterns and properties in multiple aligned protein sequences. Bioinformatics 16:950–951PubMedCrossRefGoogle Scholar
  44. 44.
    Sebastian W, Reiche K, Hofacker IL, Stadler PF, Backofen R (2007) Inferring non-coding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comput Biol 3(4):e65CrossRefGoogle Scholar
  45. 45.
    Stothard P (2000) The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences. Biotechniques 28:1102–1104PubMedGoogle Scholar
  46. 46.
    Lassmann T, Sonnhammer ELL (2006) Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment. Nucleic Acids Res 34: W596–W599PubMedCrossRefGoogle Scholar
  47. 47.
    Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797PubMedCrossRefGoogle Scholar
  48. 48.
    Tsai YT, Huang YP, Yu CT, Lu CL (2004) MuSiC: a tool for multiple sequence alignment with constraints. Bioinformatics 20:2309–2311PubMedCrossRefGoogle Scholar
  49. 49.
    DeSantis TZ Jr, Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM et al (2006) NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 34: W394–W399PubMedCrossRefGoogle Scholar
  50. 50.
    Rognes T (2001) ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches. Nucleic Acids Res 29:1647–1652PubMedCrossRefGoogle Scholar
  51. 51.
    Sæbø PE, Andersen SM, Myrseth J, Laerdahl JK, Rognes T (2005) PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology. Nucleic Acids Res 33:W535–W539PubMedCrossRefGoogle Scholar
  52. 52.
    Rognes T, Andersen SM (2005) PARALIGN user’s guide. Sencel Bioinformatics AS, Oslo, NorwayGoogle Scholar
  53. 53.
    Notredame C, Higgins DG, Heringa J (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 302:205–217PubMedCrossRefGoogle Scholar
  54. 54.
    Mignone F, Horner DS, Pesole G (2004) WebVar: a resource for the rapid estimation of relative site variability from multiple sequence alignments. Bioinformatics 20:1331–1333PubMedCrossRefGoogle Scholar
  55. 55.
    Noe L, Kucherov G (2005) YASS: enhancing the sensitivity of DNA similarity search. Nucleic Acids Res 33:W540–W543PubMedCrossRefGoogle Scholar
  56. 56.
    Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882PubMedCrossRefGoogle Scholar
  57. 57.
    Higgins DG, Sharp PM (1988) CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73:237–244PubMedCrossRefGoogle Scholar
  58. 58.
    Sze SH, Lu Y, Yang Q (2006) A polynomial time solvable formulation of multiple sequence alignment. J Comput Biol 13:309–319PubMedCrossRefGoogle Scholar
  59. 59.
    Higgins DG, Bleasby AJ, Fuchs R (1992) CLUSTAL V: improved software for multiple sequence alignment. Comput Appl Biosci 8:189–191PubMedGoogle Scholar
  60. 60.
    Higgins DG, Thompson JD, Gibson TJ (1996) Using CLUSTAL for multiple sequence alignments. Methods Enzymol 266:383–402PubMedCrossRefGoogle Scholar
  61. 61.
    Notredame C (2001) User documentation and F.A.Q. T-COFFEE (1.35) MOCCA. Accessed 10 Sept 2011
  62. 62.
    Poirot O, O’Toole E, Notredame C (2003) Tcoffee@igs: a web server for computing, evaluating and combing multiple sequence alignment. Nucleic Acids Res 31:3503–3506PubMedCrossRefGoogle Scholar
  63. 63.
    Liu L, Pearl DK (2007) Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst Biol 56:504–514PubMedCrossRefGoogle Scholar
  64. 64.
    Edwards SV, Liu L, Pearl DK (2007) High resolution species trees without concatenation. PNAS 104:5936–5941PubMedCrossRefGoogle Scholar
  65. 65.
    Ronquist F, Huelsenbeck JP (2003) MrBayes version 3.0: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574PubMedCrossRefGoogle Scholar
  66. 66.
    Liu L (2008) BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics 24:2542–2543PubMedCrossRefGoogle Scholar
  67. 67.
    Liu L, Pearl DK, Brumfield RT, Edwards SV (2008) Estimating species trees using multiple-allele DNA sequence data. Evolution 62:2080–2091PubMedCrossRefGoogle Scholar
  68. 68.
    Brito PH, Edwards SV (2009) Multilocus phylogeography and phylogenetics using sequence-based markers. Genetica 135:439–455PubMedCrossRefGoogle Scholar
  69. 69.
    Nichols R (2001) Gene trees and species trees are not the same. Trends Ecol Evol 16:358–364PubMedCrossRefGoogle Scholar
  70. 70.
    Rannala B, Yang Z (2003) Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164:1645–1656PubMedGoogle Scholar
  71. 71.
    Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1953) Equations of state calculations by fast computing machines. J Chem Phys 21:1087–1091CrossRefGoogle Scholar
  72. 72.
    Huelsenbeck JP (2002) Testing a covariotide model of DNA substitution. Mol Biol Evol 19:698–707PubMedCrossRefGoogle Scholar
  73. 73.
    Hastings WK (1970) Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57:97–109CrossRefGoogle Scholar
  74. 74.
    Larget B, Simon D (1999) Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol Biol Evol 16:750–759CrossRefGoogle Scholar
  75. 75.
    Yang Z, Rannala B (1997) Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte carlo method. Mol Biol Evol 14:717–724PubMedCrossRefGoogle Scholar
  76. 76.
    Romeralo M, Baldauf SL, Cavender JC (2009) A new species of cellular slime mold from southern Portugal based on morphology, ITS and SSU sequences. Mycologia 101:269–274PubMedCrossRefGoogle Scholar
  77. 77.
    Huelsenbeck JP, Ronquist F (2001) MrBayes: Bayesian inference in phylogenetic trees. Bioinformatics 17:754–755PubMedCrossRefGoogle Scholar
  78. 78.
    Swofford DL, Olsen GJ, Waddell PJ, Hillis DM (1996) Phylogenetic inference. In: Hillis DM, Moritz C, Mable BK (eds) Molecular systematics. Sinauer Associates, Sunderland, MA, pp 407–514Google Scholar
  79. 79.
    Wilgenbusch JC, Swofford D (2003) Inferring evolutionary trees with PAUP*. Curr Protoc Bioinformatics 6:21–28Google Scholar
  80. 80.
    Swofford DL (2002) PAUP*. Phylogenetic analysis using parsimony (*and other methods). Sinauer Associates, Sunderland, USAGoogle Scholar
  81. 81.
    Overton BE, Stewart EL, Geiser DM, Jaklitsch WM (2006) Systematics of Hypocrea citrina and related taxa. Stud Mycol 56:11–38Google Scholar
  82. 82.
    Huang T, Yeh Y, Tzeng DD (2010) Heteroduplex mobility assay for identification and phylogenetic analysis of anthracnose fungi. J Phytopathol 158:46–55CrossRefGoogle Scholar
  83. 83.
    Grünig CR, Duò A, Sieber T, Holdenrieder O (2008) Assignment of species rank to six reproductively isolated cryptic species of the Phialocephala fortinii s.l.-Acephala applanata species complex. Mycologia 100:47–67PubMedCrossRefGoogle Scholar
  84. 84.
    Sung G, Sung J, Hywel-Jones NL, Spatafora JW (2007) A multi-gene phylogeny of Clavicipitaceae (Ascomycota, Fungi): identification of localized incongruence using a combinational bootstrap approach. Mol Phylogenet Evol 44:1204–1223PubMedCrossRefGoogle Scholar
  85. 85.
    Brenn N, Menkis A, Grünig CR, Sieber TN, Holdenrieder O (2008) Community structure of Phialocephala fortiniis. lat. in European tree nurseries, and assessment of the potential of the seedlings as dissemination vehicles. Mycol Res 112:650–662PubMedCrossRefGoogle Scholar
  86. 86.
    Bomberg M, Timonen S (2009) Effect of tree species and mycorrhizal colonization on the archaeal population of Boreal Forest rhizospheres. Appl Environ Microbiol 75:308–315PubMedCrossRefGoogle Scholar
  87. 87.
    Grebenc T, Martín MP, Kraigher H (2009) Ribosomal ITS diversity among the European species of the genus Hydnum (Hydnaceae). Anales del Jardín Botánico de Madrid 66S1:121–132CrossRefGoogle Scholar
  88. 88.
    Maddison DR, Maddison WP (2000) MacClade 4: analysis of phylogeny and character evolution. Version 4.0. Sinauer Associates, Sunderland, MassachusettsGoogle Scholar
  89. 89.
    Simmons MP, Bailey CD, Nixon KC (2000) Phylogeny reconstruction using duplicate genes. Mol Biol Evol 17:469–473PubMedCrossRefGoogle Scholar
  90. 90.
    Wang Z, Nilsson RH, Lopez-Giraldez F, Zhuang W, Dai Y, Johnston PR et al (2011) Tasting soil fungal diversity with earth tongues: phylogenetic test of SATé alignments for environmental ITS data. PLoS One 6:e19039PubMedCrossRefGoogle Scholar
  91. 91.
    James TY, Letcher PM, Longcore JE, Mozley-Standridge SE, Porter D, Powell MJ et al (2006) A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota). Mycologia 98:860–871PubMedCrossRefGoogle Scholar
  92. 92.
    Little AEF, Currie CR (2007) Symbiotic complexity: discovery of a fifth symbiont in the attine ant–microbe symbiosis. Biol Lett 3:501–504PubMedCrossRefGoogle Scholar
  93. 93.
    Kim SY, Park SY, Ko KS, Jung HS (2003) Phylogenetic analysis of Antrodia and related taxa based on partial mitochondrial SSU rDNA sequences. Antonie Van Leeuwenhoek 83:81–88PubMedCrossRefGoogle Scholar
  94. 94.
    Suh S, Noda H, Blackwell M (2001) Insect symbiosis: derivation of yeast-like endosymbionts within an entomopathogenic filamentous lineage. Mol Biol Evol 18:995–1000PubMedCrossRefGoogle Scholar
  95. 95.
    Schultz TR, Brady SG (2008) Major evolutionary transitions in ant agriculture. PNAS 105: 5435–5440PubMedCrossRefGoogle Scholar
  96. 96.
    Reeb V, Lutzoni F, Roux C (2004) Contribution of RPB 2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory. Mol Phylogenet Evol 32:1036–1060PubMedCrossRefGoogle Scholar
  97. 97.
    Lutzoni F, Kauff F, Cox CJ, McLaughlin D, Celio G, Dentinger B et al (2004) Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. Am J Bot 91:1446–1480PubMedCrossRefGoogle Scholar
  98. 98.
    Bidochka MJ, St Leger RJ, Stuart A, Gowanlock K (1999) Nuclear rDNA phylogeny in the fungal genus Verticillium and its relationship to insect and plant virulence, extracellular proteases and carbohydrases. Microbiology 145:955–963PubMedCrossRefGoogle Scholar
  99. 99.
    U’ren JM, Dalling JW, Gallery RE, Maddison DR, Davis EC, Gibson CM et al (2009) Diversity and evolutionary origins of fungi associated with seeds of a neotropical pioneer tree: a case study for analysing fungal environmental samples. Mycol Res 113:432–449PubMedCrossRefGoogle Scholar
  100. 100.
    Berbee ML (2001) The phylogeny of plant and animal pathogens in the Ascomycota. Physiol Mol Plant Pathol 59:165–187CrossRefGoogle Scholar
  101. 101.
    Gerardo NM, Mueller UG, Price SL, Currie CR (2004) Exploiting a mutualism: parasite specialization on cultivars within the fungus-growing ant symbiosis. Proc Biol Sci 271:1791–1798PubMedCrossRefGoogle Scholar
  102. 102.
    Schmidt HA (2009) Testing tree topologies. In: Lemey P, Salemi M, Vandamme AM (eds) The phylogenetic handbook: a practical approach to phylogenetic analysis and hypothesis testing. Cambridge University Press, Cambridge, U.K., pp 381–404CrossRefGoogle Scholar
  103. 103.
    Schmidt HA, von Haeseler A (2009) Phylogenetic inference using maximum likelihood methods. In: Lemey P, Salemi M, Vandamme AM (eds) The phylogenetic handbook: a practical approach to phylogenetic analysis and hypothesis testing. Cambridge University Press, Cambridge, U.K., pp 181–209CrossRefGoogle Scholar
  104. 104.
    Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376PubMedCrossRefGoogle Scholar
  105. 105.
    Felsenstein J (1988) Phylogenies from molecular sequences: inference and reliability. Annu Rev Genet 22:521–565PubMedCrossRefGoogle Scholar
  106. 106.
    Kishino H, Hasegawa M (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J Mol Evol 29:170–179PubMedCrossRefGoogle Scholar
  107. 107.
    Strimmer K, von Haeseler A (1996) Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol Biol Evol 13:964–969CrossRefGoogle Scholar
  108. 108.
    Strimmer K, Goldman N, von Haeseler A (1997) Bayesian probabilities and quartet puzzling. Mol Biol Evol 14:210–213CrossRefGoogle Scholar
  109. 109.
    Strimmer K, von Haeseler A (1997) Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. Proc Natl Acad Sci U S A 94:6815–6819PubMedCrossRefGoogle Scholar
  110. 110.
    Trelles O (2001) On the parallelisation of bioinformatics applications. Brief Bioinform 2:181–194PubMedCrossRefGoogle Scholar
  111. 111.
    Schmidt HA, Petzold E, Vingron M, von Haeseler A (2003) Molecular phylogenetics: parallelized parameter estimation and quartet puzzling. J Parallel Distrib Comput 63:719–727CrossRefGoogle Scholar
  112. 112.
    Schmidt HA, Strimmer K, Vingron M, von Haeseler A (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502–504PubMedCrossRefGoogle Scholar
  113. 113.
    Petzold E, Merkle D, Middendorf M, von Haeseler A, Schmidt HA (2006) Phylogenetic parameter estimation on COWs. In: Zomaya AY (ed) Parallel computing for bioinformatics and computational biology. John Wiley & Sons, New York, pp 347–368Google Scholar
  114. 114.
    Page RDM (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  1. 1.Department of BotanyKarnataka UniversityDharwadIndia
  2. 2.Department of ZoologyKarnataka UniversityDharwadIndia

Personalised recommendations