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Biology 695, Advanced Molecular Phylogenetics, Spring 2019.




Time and Location: Monday from 24 PM in B205.

Instructors:
  • Dr. Hazel Barton,      Dr. Stefan Forcey

    • Office hours:
      • Forcey: M 11:15am-12:30pm, WF 1:15pm-2:30pm, CAS 275.


    Here's an approximate schedule of what we'll be doing this semester. Emphasis on the "approximate". All lecture slides created by Dr. Barton.

    Jan. 14: Day one.

    Week 1 Lecture

    Jan. 21: No class on Martin Luther King day.

    Week 2 Lecture, with clickable links to sequence databases.

    Week 3 Lecture

    Week 4 Lecture

    Week 5 Lecture

    Week 6 Lecture

    Mar. 25-29: Spring break.
    April 29: Last day.


    Homework
    HW1 due Feb 3.

    Resources

    I. Links to software sites:

      Sequence Conversion:
    1. EMBOSS
    2. MABL
    3. Los Alamos

    4. Trees:
    5. Phylogeny.fr
    6. TreeView

    7. Stats:
    8. R;
      phangorn package for R;
      ape package for R;
    9. MrBayes
    10. PhyML
    11. PHYLIP

    12. Geometry:
    13. polymake

    II. Links to computing resources:

    1. Installing software
    2. UNIX Tutorial
    3. Using Emacs
    4. Quality assessment of NGS data
    5. Barcodes for QIIME tutorial
    6. File format conversions
    7. File formats
    8. Glossary

    III. Supplemental Resources:

    1. On the optimality of the neighbor-joining algorithm by Eickmeyer, et al (2009)
      On the optimality of the neighbor-joining algorithm_Eickmeyer et al
    2. Geometry of the neighbor-joining algorithm for small trees by Eickmeyer and Yoshida
      Geometry of Neighbor Joining Algo for Small Trees _Yoshida et al_0908.0098v1
    3. Haws, Hodge and Yoshida (2012)
      HHY_Optimality of NJ Algo and Faces of BME_Bull Math Biol
    4. Theoretical Foundation of the Balanced Minimum Evolution Method of Phylogenetic Inference
      and Its Relationship to Weighted Least-Squares Tree Fitting by Desper and Gascuel (2004)
      Theoretical foundation of BME_Desper and Gascuel
    5. Neighbor-Joining Revealed by Gascuel and Steel (2006)
      Neighbor-Joining Revealed_Gascuel and Steel_2006
    6. Semple and Steel paper giving generalization of Pauplin’s formula to non-binary trees:
      Cyclic permutations and evolutionary trees_Semple and Steel
    7. Combinatorics of Least Squares Trees:
      Combinatorics of least squares trees_Pachter et al
    8. A great resource is wolfram|alpha.
      Here is a function whose power series has coefficients the triangular numbers, n choose 2.

    9. For sequences: the Online Encyclopedia of Integer Sequences
      Here is the open question of counting numbers of posets.
      Here is the open question of counting numbers of polyhedra.



    CREDIT:
    The text of this page was adapted, with permission, from an original course site by J.P. Cossey. Links to resources were collected by Terrell Hodge for the Working Group on phylogenetics at the Winthrop NSF/CBMS Conference on Mathematical Phylogeny in 2014.