Brian Thomas Foley

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Questions related from Brian Thomas Foley

How do you measure phylogenetic signal vs noise in a multiple sequence alignment?

I know of a couple of measures of signal:noise ration in phylogenetic analyses, such as the consistency index and the retention index, but most phylogenetic reconstruction software packages do not...

09 September 2014 5,515 6 View

What is the largest known protien?

Today I came across a 5,224 amino acid long protein, from Drosphila, that has homologs in other insects. http://www.ncbi.nlm.nih.gov/nuccore/194894863 It is some sort of fancy zinc finger protein...

04 April 2014 661 1 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...

01 January 2014 7,688 19 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...

12 December 2013 9,761 5 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,...

04 April 2013 9,460 7 View

Is there a tool for annotation-assisted multiple sequence alignment?

At the HIV Sequence and Immunolgogy Databases where I work, we have used a bit of creativity to solve some difficult problems in multiple sequence alignment. Often we want to produce an alignment...

04 April 2013 944 5 View

Is this good advice for a student or post-doc doing bioinformatics in a traditional "wet bench" biology group?

It is sort of a rhetorical question, about this advice I came across...

04 April 2013 9,136 5 View

How to fix a phylogenetic tree, long branches attract problem?

With HIV-1 phylogenies we quite often have data sets where we know important details about the true evolutionary history. For one example, with a local transmission chain such as husband to wife...

01 January 1970 967 10 View

Would this paper be good for your project?

Would this paper be a good addition to your project: https://www.researchgate.net/publication/324212102_The_evolutionary_history_of_vertebrate_RNA_viruses The evolutionary history of vertebrate...

01 January 1970 957 2 View