You can download these binaries

• APE Paradis E., Claude J., Strimmer K.
  Analyses of Phylogenetics and Evolution in R language
• Bio++ Dutheil J. et al.
  Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics
• Bio++ Program Suite Dutheil J.
  A set of programs for phylogenetic trees reconstruction
• BIONJ Gascuel O.
  Improved version of NJ, based on a model of sequence data
• DTscore Elemento O., Gascuel O.
  Distance based algorithm to reconstruct the duplication history of tandemly repeated sequences
• FastME Desper R., Gascuel O.
  Distance based phylogeny reconstruction algorithm
• Genepop Rousset F.
  Classical population genetic tests and various more focused applications (e.g. inferences under isolation by distance)
• GENETIX Belkhir K., Borsa P., Chikhi L., Raufaste N., Bonhomme F.
  Set of programs to compute several basic parameters of population genetics
• MPscan Rivals E., Kalsi P., Salmela L., Kiiskinen P., Tarhio J.
  Fast localisation of multiple reads in genomes
• New phylogenetic models for the evolution of proteins Quang L.S., Gascuel O., Lartillot N.
• NHML Galtier N., Gouy M.
  Programs for maximum-likelihood phylogenetic inferences
• Partition Dawson K., Belkhir K.
  Bayesian identification of population sub-division
• PermutMatrix Caraux G., Pinloche S.
  Graphical software for analyzing and visualizing gene expression data
• PhyD* Criscuolo A., Gascuel O.
  Fast NJ-like algorithms to deal with incomplete distance matrices
• Phylo_win Galtier N., Gouy M., Gautier C.
  Graphical colour interface for molecular phylogenetic inference
• PhyloBayes Lartillot N.
  Bayesian phylogenetic software based on mixture models
• PhyML Guindon S., Gascuel O.
  Phylogenetic Maximum Likelihood
• PhySIC_IST Scornavacca C., Berry V., Lefort V., Douzery E.J.P., Ranwez V.
  Cleaning source trees to infer more informative supertrees (a recent development of the PhySIC method)
• PhySIC Ranwez V., Berry V., Criscuolo A., Fabre P.H., Guillemot S., Scornavacca C., Douzery E.J.P.
  Phylogenetic inference of Supertrees with Induction and non-Contradiction
• SDM Criscuolo A., Berry V., Douzery E.J.P., Gascuel O.
  Fast Distance-based Approach for (Super)Tree Building in Phylogenomics
• SSIMUL Scornavacca C., Berry V., and Ranwez V.
  Speciation SIgnal extraction from MULtigene families
• STAR Delgrange O., Rivals E.
  Algorithm to Search for Tandem Approximate Repeats
• TreeDyn Chevenet F., Brun C., Banuls A.L., Jacq B., Christen R.
  Towards dynamic graphics and annotations for analyses of trees