STEM Species Tree Estimation using Maximum likelihood
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STEM Ranking & Summary

STEM Tags

analysis Cost Estimation estimation Time estimation Motion Estimation maximum CFF3 estimation species gene bird species software estimation parameter estimation disparity estimation Cetacea species create species generate species FDR estimation haplotype estimation species tree species monitor performance estimation Estimation Creator osmosis estimation hierarchical likelihood phylogenetic tree estimation model parameters estimation large phylogeny estimation large phylogenies estimation Branch Length gene tree tree estimation maximum likelihood allele duct estimation effort estimation print estimation maximum linkdepth

STEM Description

STEM was developed to be a program for inferring maximum likelihood species trees from a collection of estimated gene trees under the coalescent model. The program will either return the exact ML tree, compute the likelihood for a user-specified tree, or search for a set of highest likelihood trees. The method for searching the space of trees is a simulated annealing algorithm. STEM requires several input files. The first of these is the file which gives the information for the gene trees, which must be called genetrees.tre. This file contains the gene trees with branch lengths in Newick format. Gene trees must be rooted and must satisfy the molecular clock, although the program won’t check for this (you will likely get an error or it will run indefinitely if this it not the case). Directly in front of each gene tree is a number within square brackets that gives the rate multiplier for each gene.

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