Citing CLIME

Y. Li, S.E. Calvo, R. Gutman, J.S. Liu, and V.K. Mootha (2014) Expansion of biological pathways based on evolutionary inference, Cell 158, 213–225. Pubmed: 24995987

Y. Li, S. Ning, S.E. Calvo, V.K. Mootha and J.S. Liu (2018) Bayesian hidden Markov tree models for clustering genes with shared evolutionary history, The Annals of Applied Statistics, in press. arXiv: 1808.06109



CLIME software (including users' manual)

Pre-computed CLIME analyses of published gene sets

PDF TXT Human complex I
PDF TXT Human ciliary genes
PDF TXT Human mitochondrial genes
PDF TXT All 5331 P. falciparum genes
PDF TXT All 5013 C. merolae genes
PDF TXT All 5882 S. cerevisiae genes
1025 human pathways from GO and KEGG

Phylogenetic profile matrices for 10 model organisms across 138 eukaryotes (plus Prokaryote outgroup)

hsa.matrix138.txt H. sapiens phylogenetic matrix
mmu.matrix138.txt M. musculus phylogenetic matrix
dme.matrix138.txt D. melanogaster phylogenetic matrix
cel.matrix138.txt C. elegans phylogenetic matrix
ncr.matrix138.txt N. crassa phylogenetic matrix
sce.matrix138.txt S. cerevisiae phylogenetic matrix
ath.matrix138.txt A. thaliana phylogenetic matrix
cme.matrix138.txt C. merolae phylogenetic matrix
pfa.matrix138.txt P. falciparum phylogenetic matrix
tbr.matrix138.txt T. brucei phylogenetic matrix
euk138.with_prok.nwk Tree topology for 138 eukaryotes plus prokaryote outgroup, in Newick format

Last updated 10/18/2022