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Phylogenetics

Tue, 2007-05-22 22:06 — alf

If you had 100,000 DNA sequences, each 1000 nucleotides long, and you wanted to cluster them or create a phylogeny, which software would you use?

Also, what if they were amino acid sequences, rather than nucleotides?


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Thu, 2007-05-31 07:07 — jason

quicktree

I'd use MAFFT for aligning something this big.
quicktree was designed for building trees from large datasets like this (Pfam families).


Fri, 2007-06-01 01:04 — nuin

MAFFT

Yep, MAFFT is fast and has excellent alignment quality. My last year's paper showed that it is the best for prtein alignment, even for distant sequences.


Tue, 2007-05-29 00:07 — nuin

Phylip

Apart from CD-HIT which is a very good software, I would try using Phylip. The sequences are not large but the actual number of sequences is the problem. Try using a Neighbor Joining approach in Phylip, it won't be blazing fast but it will do the job, eventually.

I used Phylip to build a NJ tree of a set of 20000 protein sequences and it took me around 3-4 weeks to get it done on a 3GHz Xeon machine.


Sat, 2007-05-26 21:48 — Neil

cd-hit

For clustering, CD-HIT is excellent. Very fast, handles many sequences. Used to create the non-redundant datasets in UniProt and at the PDB.

Phylogeny - I've never gone much beyond Clustal and Phylip, both of which would take hours on an average machine with any more than a few thousand sequences. I've heard good things about MrBayes - which is MPI-enabled, so could run on a cluster if you have access to one.


Sat, 2007-05-26 13:25 — Animesh

Huge!

Alf that is a huge requirement! Are you trying to make tree of life with 1000 base upstream of some house-keeping genes?
I think MUSCLE [ http://www.drive5.com/muscle/ ] can come to rescue, but you would need a good machine for sure. It uses log-expectation as profile function which is faster and accurate as well [ http://www.biomedcentral.com/1471-2105/5/113/table/T2 ]. General algorithm is http://nar.oxfordjournals.org/content/vol32/issue5/images/large/gkh340f2... .
More details in the paper http://nar.oxfordjournals.org/cgi/content/full/32/5/1792 .

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