Brian Thomas Foley

6 Questions 481 Answers 0 Followers

Questions related from Brian Thomas Foley

Is there a program for aligning circular DNA, small plasmids, which have different sites of linearization for GenBank entries?

Many bacterial complete genomes have been sequenced with small plasmids of less than 5kb. If I use BLAST to search for plasmids similar to my plasmid of interest, I find a few dozen, but some are...

20 December 2016 678 5 View

What is a good tool for pulling complete genes from chromosomes/contigs/genomes?

I have aligned the complete mitochondrial genomes of well over 200 vertebrates, mostly mammals with some birds, reptiles, amphibians, fish for outgroups. The mitochondrial DNA evolves about...

10 January 2014 8,412 18 View

What are some of the best Phylogenetics/ Evolution textbooks out today, for undergraduate and PhD level?

A Google search for "Phylogenetics Textbook" brings up several titles of books, and some online courses etc. Can any of you add information about which books you have used and why you like them or...

27 December 2013 7,848 4 View

Is the montreme/marsupial/mammal root so deep?

In this paper: The delayed rise of present-day mammals. Bininda-Emonds OR, Cardillo M, Jones KE, MacPhee RD, Beck RM, Grenyer R, Price SA, Vos RA, Gittleman JL, Purvis A. Nature. 2007 Mar...

16 August 2013 8,347 4 View

Does any one have more information to support the claim that there are two-fold more retroviral elements in human genome than chimpanzee?

I find this difficult to believe, and even more difficult to verify: http://jrs.sagepub.com/content/97/12/560.long "... Retrovirus-related elements massively repeated in the human genome include...

29 June 2013 8,841 2 View

Is the devil in the details?

Point mutations are a small part of evolution overall. Gene duplications and acquisition of genes by horizontal transfer is larger. Sex and recombination, genetic bottlenecks, population sizes,...

27 April 2013 1,253 6 View