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The MP-EST method estimates species trees from a set of gene trees by maximizing a pseudo-likelihood function. The input gene trees must be bifurcating rooted trees (w/o branch lengths) in Newick format, for example, the ML trees generated from PHYML, RAXML, or PHYLIP and rooted with the outgroup species. The MP-EST method allows missing taxa in some gene trees. The examples of the input files are available here. When multiple alleles (or sequences) are sampled from some species, the user must provide a species-allele table to indicate which alleles belong to which species. For example, the following gene trees have taxa S1 - 6.

(((((S1:0.1,S2:0.1):0.1,S4:0.1):0.1,S3:0.1):0.1,S5:0.1):0.1,S6:0.2);
(((((S1:0.1,S2:0.1):0.1,S4:0.1):0.1,S5:0.1):0.1,S3:0.1):0.1,S6:0.2);
(((((S1:0.1,S2:0.1):0.1,S4:0.1):0.1,S3:0.1):0.1,S5:0.1):0.1,S6:0.2);

Suppose S1 and S2 were sampled from Human, S3 and S4 were sampled from Ape, S5 were sampled from Gorilla, and S6 was sampled from Chimpanzee. Then the species-allele table may be

H	2	S1 S2
A	2	S3 S4
G	1	S5
C	1	S6

Each line specifies "the species name", "the number of alleles", "the names of the alleles". Note that you could use any names as the species names. For help, click here. If each species has only one allele (or sequence), you do not need to provide this table. Just upload the gene tree file and click "submit". When multiple alleles were sampled, please provide the species-allele table in the textbox and then upload the tree file and click "submit".