I. Links to software sites:
Sequence Conversion:
 EMBOSS
 MABL
 Los Alamos
Trees:
 Phylogeny.fr
 TreeView
Stats:
 R;
phangorn package for R;
ape package for R;
 MrBayes
 PhyML
 PHYLIP
Geometry:
 polymake
II. Links to computing resources:

Installing software
 UNIX Tutorial
 Using Emacs
 Quality assessment of NGS data
 Barcodes for QIIME tutorial
 File format conversions
 File formats
 Glossary
III. Supplemental Resources:
 On the optimality of the neighborjoining algorithm by Eickmeyer, et al (2009)
On the optimality of the neighborjoining algorithm_Eickmeyer et al
 Geometry of the neighborjoining algorithm for small trees by Eickmeyer and Yoshida
Geometry of Neighbor Joining Algo for Small Trees _Yoshida et al_0908.0098v1
 Haws, Hodge and Yoshida (2012)
HHY_Optimality of NJ Algo and Faces of BME_Bull Math Biol
 Theoretical Foundation of the Balanced Minimum Evolution Method of Phylogenetic Inference
and Its Relationship to Weighted LeastSquares Tree Fitting by Desper and Gascuel (2004)
Theoretical foundation of BME_Desper and Gascuel
 NeighborJoining Revealed by Gascuel and Steel (2006)
NeighborJoining Revealed_Gascuel and Steel_2006
 Semple and Steel paper giving generalization of Pauplin’s formula to nonbinary trees:
Cyclic permutations and evolutionary trees_Semple and Steel
 Combinatorics of Least Squares Trees:
Combinatorics of least squares trees_Pachter et al
 A great resource is wolframalpha.
Here is a function whose power series has coefficients the triangular numbers, n choose 2.
 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.