Fastphylo to calculate distance matrices for filtering?

[nhoffman]

Might be a faster alternative to fasttree (looks like it requires aligned sequences)

http://www.biomedcentral.com/1471-2105/14/334

Fastphylo: Fast tools for phylogenetics

"We present fastphylo, a software package containing implementations of efficient algorithms for two common problems in phylogenetics: estimating DNA/protein sequence distances and reconstructing a phylogeny from a distance matrix. We compare fastphylo with other neighbor joining based methods and report the results in terms of speed and memory efficiency."

[cmccoy]

I believe that FastTree is sub-quadratic, so fastphylo is likely to be
slower if it creates and operates on a distance matrix.

On Mon, Dec 9, 2013 at 3:30 PM, Noah Hoffman notifications@github.comwrote:

Might be a faster alternative to fasttree (looks like it requires aligned
sequences)

http://www.biomedcentral.com/1471-2105/14/334

Fastphylo: Fast tools for phylogenetics

"We present fastphylo, a software package containing implementations of
efficient algorithms for two common problems in phylogenetics: estimating
DNA/protein sequence distances and reconstructing a phylogeny from a
distance matrix. We compare fastphylo with other neighbor joining based
methods and report the results in terms of speed and memory efficiency."

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/6
.

Connor McCoy
Fred Hutchinson Cancer Research Center
1100 Fairview Ave N.
Seattle, WA 98109-1924
cmccoy@fhcrc.org

[matsen]

Yep. It would be useful in some application where you need the distances
themselves (e.g. regression) or you are given a distance matrix and want to
make a tree. I don't think that's us though.

On Mon, Dec 9, 2013 at 3:51 PM, Connor McCoy notifications@github.comwrote:

I believe that FastTree is sub-quadratic, so fastphylo is likely to be
slower if it creates and operates on a distance matrix.

On Mon, Dec 9, 2013 at 3:30 PM, Noah Hoffman notifications@github.comwrote:

Might be a faster alternative to fasttree (looks like it requires
aligned
sequences)

http://www.biomedcentral.com/1471-2105/14/334

Fastphylo: Fast tools for phylogenetics

"We present fastphylo, a software package containing implementations of
efficient algorithms for two common problems in phylogenetics:
estimating
DNA/protein sequence distances and reconstructing a phylogeny from a
distance matrix. We compare fastphylo with other neighbor joining based
methods and report the results in terms of speed and memory efficiency."

—
Reply to this email directly or view it on GitHub<
https://github.com/fhcrc/deenurp/issues/6>
.

Connor McCoy
Fred Hutchinson Cancer Research Center
1100 Fairview Ave N.
Seattle, WA 98109-1924
cmccoy@fhcrc.org

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/6#issuecomment-30186731
.

Frederick "Erick" Matsen, Assistant Member
Fred Hutchinson Cancer Research Center
http://matsen.fhcrc.org/

[nhoffman]

FWIW, we do use the distances themselves to calculate centroids and outliers - this is calculated using FastTree -nt -makematrix seqs.fasta. It isn't really clear to me from the docs or help text what, exactly, these distances represent (ie, sum of branch lengths between leaves vs pairwise distances of some sort - log-corrected distances, perhaps?).

[cmccoy]

Ah, my apologies for closing then.