Software

  • jMODELTEST 2: High Performance Computing selection of models of nucleotide substitution. (jmodeltest.org server)
  • PROTTEST 3: High Performance Computing selection of empirical models of aminoacid replacement¬†
  • ProtASR: Ancestral sequence reconstruction of proteins accounting for structural constraints.
  • CoalEvol: Simulation of DNA/codon/aa sequences under different population models.
  • SGWE: Simulation of genome-wide evolution using CoalEvol.
  • CodABC: Coestimation of recombination, substitution and dN/dS using approximate Bayesian computation.
  • ALTER WEB SERVER: Program-oriented alignment format converter.
  • NETRECODON: Simulation of coding sequences with intracodon recombination, migration and growth.
  • GEODIS:¬† Nested clade phylogeographic analysis (NCPA).
  • TREESCAN: Genotype/phenotype association test upon a haplotype tree.
  • TCS: Reconstruction of phylogenetic networks from DNA sequences using statistical parsimony.

  • RDP¬†is a Windows program developed by Darren Martin for the detection of recombination from DNA alignments. It includes several methods, like RDP, MaxChi, Chimaera, Geneconv, Bootscan and Siscan. Current version is Beta 0.8