Phylogenetic Analysis Programs
User Guide
Embedded Tools
Site History

Embedded tools

  • Ensembl
    Flicek, P., B. L. Aken, et al. (2009).
    Ensembl's 10th year.
    Nucleic Acids Res 38(Database issue): D557-62.
  • Muscle
    Edgar, R. C. (2004).
    MUSCLE: a multiple sequence alignment method with reduced time and space complexity.
    BMC Bioinformatics 5(113): 113.
    Loytynoja and Goldman (2010).
    webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser.
    BMC Bioinformatics 11(1): 579.
    Suyama, M., D. Torrents, et al. (2006).
    PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments.
    Nucleic Acids Res 34(Web Server issue): W609-12.
  • Gblocks
    Talavera, G. and J. Castresana (2007).
    Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments.
    Syst Biol 56(4): 564-77.
  • TreeBest
    L. Heng, A.J. Vilella, E. Birney, and R. Durbin
  • Archaeopteryx
    Han M.V. and Zmasek C.M. (2009).
    phyloXML: XML for evolutionary biology and comparative genomics.
    BMC Bioinformatics 10(356): 356.
  • PAML
    Yang, Z. (2007).
    PAML 4: phylogenetic analysis by maximum likelihood.
    Mol Biol Evol 24(8): 1586-91.
  • PDB
    Berman, H. M., J. Westbrook, et al. (2000).
    The Protein Data Bank.
    Nucleic Acids Res 28(1): 235-42.
  • Modeller
    Eswar, N., D. Eramian, et al. (2008).
    Protein structure modeling with MODELLER.
    Methods Mol Biol 426: 145-59.
  • JalView
    Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009).
    Jalview Version 2 - a multiple sequence alignment editor and analysis workbench
    Bioinformatics 25 (9) 1189-1191 doi: 10.1093/bioinformatics/btp033
  • Jmol
    Herráez, A. (2006).
    Biomolecules in the computer: Jmol to the rescue.
    Biochemistry and Molecular Biology Education, 34: 255?261. doi: 10.1002/bmb.2006.494034042644