Ana Rojas Mendoza
Structural Bioinformatics Group.
Centro Nacional Investigaciones Oncológicas (CNIO Madrid).

Sardinia,June-06

Resources

The list The Felsenstein's list.
Treebase.

Servers to run/draw trees

ClustalW/Phylip servers.
Probabilistic models.
Sequence polymorphims.
Phyloblast.
Phylodendron.

Programs

DualBrothers.
Bayesian.
MrBayesCOOL.
SSa Maximum likelihood.
AsaturA Deals with saturation in aa sequences.
PHASE For RNA secondary structures.
Phylip programs.
MEGA.

Tree Drawing tools

TreeViewSimple and easy.
TrePlot Plotter.
PhyloDraw.
a Perl script by Julian Gough.
BOSQUE.
NJ plot.
ATV Java based.
Perl scripts.

Examples of alignment formats

  1. An example of a Nexus format for program Mr.Bayes
  2. Here a TOOL To CONVERT FORMATS

Some exercises:

  1. Problem 0
    • Run a phylogentic (NJ) analyses with 1000 bootstrap replicates
    • Runa a Minimum evolution analyses with 1000 bootstrap replicates
    • >>>>> ARE THEY DIFFERENT?
    • Now:
    • Change the default parameters to:
      1. p-distance first (then JTT matrix).
      2. rates to gamma (2.0 or 1.0).
      3. Change the gap option from complete to pairwise.
    • RUN NJ and ME with bootstrap (1000).
    • >>>>>>> How do these changes affect the outcome?
  2. problem 1
    • ATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGGGCGGTAGCACAGAGGAGCTTGCTCCTTGGGTG
      ACGAGCGGCGGACGGGTGAGTAATGTCTGGGGATCTGCCCGATGGAGGGGGATAACTACTGGAAACGGTA
      GCTAATACCGCATAAHCTCGCAAGAGCAAAGTGGGGGACCTTCGGGCCTCACACCATCGGATGAACCCAG
      ATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGAC
      CAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGG
      GCGCAAGCTGGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGG
      AGGAAGGCGATGTGGTTAATAACCGCGTCGATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTG
      CCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCG
      GTCTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTTGAAACTGGCAGGCTAGAGT
      CTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCG
      AAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCC
      TGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGRRCTAACG
      CGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTTGACGGGGGCCCGCAC
      AAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGCCTTGACATCCACGGAAT
      TTGGCAGAGATGCYTTAGTGCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTG
      TGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGCGTGATGGCGGGAA
      CTCAAAGGAGACTGCCGGTGATAAACCGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCTTACGGC
      CAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGAACTCGCGAGAGCAAGCGGACCTCATA
      AAGTGCGTCGTAGTCCGGATCGGAGTCTGCAACTCGACTCCGTGAAGTCGGAATCGCTAGTAATCGTAGA
      TCAGAATGCTACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGC
      AAAAGAAGTAGGTAGCTTAACTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGT
      AACAAGGAA
    • Extract a comprehensive set of sequences of different species.
    • Generate a multiple sequence alignment.
    • Use 2 different methods to construct a phylogeny.
    • What can you say about this sequence?
  3. Problem 2
    • Pick from GeneBank at least a minimum of 8 orthologous sequences (Prot or DNA).
    • Compute a good alignment.
    • Run one distance-based method against a probabilistic method.
    • Obtain bootstrap values for both methods.