The increasing availability of complete genome data is facilitating the 
acquisition of phylogenomic data sets, but the process of obtaining orthologous 
sequences from other genomes and assembling multiple sequence alignments remains 
piecemeal and arduous. We designed software that performs these tasks and 
outputs anonymous loci (AL) or anchored enrichment/ultraconserved element loci 
(AE/UCE) data sets in ready-to-analyze formats. We demonstrate our program by 
applying it to the hominoids. Starting with human, chimpanzee, gorilla, and 
orangutan genomes, our software generated an exhaustive data set of 292 ALs (∼1 
kb each) in ∼3 h. Not only did analyses of our AL data set validate the program 
by yielding a portrait of hominoid evolution in agreement with previous studies, 
but the accuracy and precision of our estimated ancestral effective population 
sizes and speciation times represent improvements. We also used our program with 
a published set of 512 vertebrate-wide AE "probe" sequences to generate data 
sets consisting of 171 and 242 independent loci (∼1 kb each) in 11 and 13 min, 
respectively. The former data set consisted of flanking sequences 500 bp from 
adjacent AEs, while the latter contained sequences bordering AEs. Although our 
AE data sets produced the expected hominoid species tree, coalescent-based 
estimates of ancestral population sizes and speciation times based on these data 
were considerably lower than estimates from our AL data set and previous 
studies. Accordingly, we suggest that loci subjected to direct or indirect 
selection may not be appropriate for coalescent-based methods. Complete in 
silico approaches, combined with the burgeoning genome databases, will 
accelerate the pace of phylogenomics.