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Recodon  v.1.6.0

Recodon simulates coding DNA sequences with recombination, migration and demographic periods. Coalescent simulations of codon models with recombination, migration and demography.

ProtTest  v.3.4

Selection of best-fit models of protein evolution. PROTTEST (ModelTest's relative) is a software for selecting the model of protein evolution that best fits a given set of sequences (alignment).

JModelTest  v.0.1.1

Phylogenetic model averaging. jMODELTEST ijModelTest is a software to carry out statistical selection of best-fit models of nucleotide substitution. It implements five different model selection strategies:

GEODIS  v.2.6

A tool to perform the nested clade phylogeographic analysis (NCPA). GEODIS is a software for the calculation of the statistics and associated P-values for the nested clade analysis (NCA) developed by Templeton and collaborators. In the NCA,

Collapse  v.1.2

Describing haplotypes from sequence alignments. COLLAPSE is a simple tool for collapsing sequences to haplotypes (unique sequences). It can read DNA sequence alignments in NEXUS or PHYLIP "sequential" format.

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