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4. Yeast Data Set

Here is the the yeast data set  data set (Rokas et al., 2003) that you could try : yeast.to analyze using our tools. It consists of 106 loci, each with a single allele sampled from seven Saccharomyces species S. cerevisiae (Scer), S. paradoxus (Spar), S. mikatae (Smik), S. kudriavzevii (Skud), S. bayanus (Sbay), S. castellii (Scas), S. kluyveri (Sklu), and the outgroup fungus Candida albicans (Calb).

The followings are the input NEXUS file you could try:

• Count the number of extra lineages given a species tree: parsimonyScoringTree
• Compute the probability of the gene trees given a species tree: probabilisticScoringTree
• Infer the species tree using parsimonious method: inferParsimoniousTree
• Infer the species tree using probabilistic method: TBA
• Count the number of extra lineages given a species network: parsimonyScoringNetwork
• Compute the probability of the gene trees given a species network: probabilisticScoringNetwork
• Infer the species network using parsimonious method: TBA
• Infer the species network using probabilistic method: TBA

5. Website

To see a full description of PhyloNet, please visit its website, where you can get the latest version of PhyloNet as well as detailed descriptions of all available commands. 

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