nodalpoint.org - Phylogenetics - Comments

MAFFT

nuin — Thu, 31 May 2007 13:04:32 -0400

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.

quicktree

jason — Wed, 30 May 2007 19:07:49 -0400

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

Phylip

nuin — Mon, 28 May 2007 12:07:55 -0400

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.

cd-hit

Neil — Sat, 26 May 2007 09:48:06 -0400

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.

Huge!

Animesh — Sat, 26 May 2007 01:25:17 -0400

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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Phylogenetics

alf — Tue, 22 May 2007 10:06:51 -0400

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?