Biology 695, Advanced Molecular Phylogenetics, Spring 2019.

I. Links to software sites:

Sequence Conversion:

1. EMBOSS
2. MABL
3. Los Alamos

Trees:

4. Phylogeny.fr
5. TreeView

Stats:

6. R;
   phangorn package for R;
   ape package for R;
7. MrBayes
8. PhyML
9. PHYLIP

Geometry:

10. 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.