Open nhoffman opened 10 years ago
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/fhcrc/deenurp/issues/6 .
Connor McCoy Fred Hutchinson Cancer Research Center 1100 Fairview Ave N. Seattle, WA 98109-1924 cmccoy@fhcrc.org
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/fhcrc/deenurp/issues/6#issuecomment-30186731 .
Frederick "Erick" Matsen, Assistant Member Fred Hutchinson Cancer Research Center http://matsen.fhcrc.org/
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?).
Ah, my apologies for closing then.
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."