tandy@ucbarpa.Berkeley.EDU (Tandy Warnow) (03/28/91)
Sampath Kannan and I have an algorithm which constructs
phylogenetic trees from DNA sequences for species. If you
have aligned sequences, please contact
Tandy Warnow
Department of Mathematics
UC Berkeley
Berkeley, CA 94720
(415) 642-3560 (office) or 644-8319 (home)
(The algorithm has been programmed and we would like to
run it on some test cases.)lloyd@bruce.cs.monash.OZ.AU (lloyd allison) (04/03/91)
In <41475@ucbvax.BERKELEY.EDU> tandy@ucbarpa.Berkeley.EDU (Tandy Warnow) writes: >Sampath Kannan and I have an algorithm which constructs >phylogenetic trees from DNA sequences for species. If you >have aligned sequences, please contact > Tandy Warnow Me too, I'd like the sequences, but shouldn't someone collect the collections. A problem like tree reconstruction needs a (large) set of standard test data. Lloyd ALLISON Department of Computer Science, UUCP:lloyd@bruce.cs.monash.edu.au Monash University, Clayton, or :uunet!munnari!bruce.cs.monash.edu.au!lloyd VICTORIA 3168, AUSTRALIA Tel :565-5205 FAX: +61 3 565 5146 PS. 1. The beta globin pseudogenes are about 2200 bp and form a "close" family often used in reconstructing the primate tree: ATRB1GLOP, GGBGLOP, HSBGLOP, ORAHBBPS, PTBGLOP 2. J. Jurka has an alignment of many "Alu" sequences, about 280bp each: jjurka@net.bio.net Family: These are Alu sequences used in study by Jerzy Jurka (Yurek Yurka) and Temple Smith, published in Proc. Natl. Acad. Sci. USA 85: 4775-4778 (1988). The sequences have been aligned by hand using sequence editor - MASE (Faulkner, D.V. and Jurka, J. TIBS 13: 321-322, 1988). The enclosed file is in the aligned output format useful for 'by eye' analysis. If you need MASE-input ... 3. %A B. F. Koop %A M. Goodman %A P. Xu %A K. Chan %A J. L. Slightom %A Primate n-globin DNA sequences and man's place among the great apes. %J Nature %P 234-238 %V 319 %D 1986 %K MolBio, DNA, gene, globin, data, string, psi, eta, globin, pseudo gene %X DNA data strings: alignment given of human, chimp, gorilla, orang utan, rhesus monkey, owl monkey and goat psi-eta globin pseudo ene %A J. Felsenstein %T Evolutionary trees from DNA sequences: a maximum likelihood approach. %J J. Mol. Evol. %V 17 %P 368-376 %D 1981 %K MolBio phylogentic tree, trees, maximum likelihood, inference %X allows for non equal rates of evolution DNA data strings: applied to 5 vertebrates' 5S RNA gives a tree, not seq's salmo, chi c, family, tree, inductive inference %A W. Bains %T The multiple origins of the human Alu sequences %J J. Mol. Evol. %V 23 %P 189-199 %D 1986 %K Alu, DNA, Phylogenetic tree, MolBio %X uses 62 Alus DNA data strings Blur 1 2 6 7 8 10 11 13 14 19 Tublin gene beta-5 A to J alpha and delta globin locus loci