Mike Keesey  

ISPN Meeting

June 20th, 2006 by Mike Keesey :: see related comic

Apologies to everyone for not being terribly regular with the essays lately. I’ve been preparing for a talk I’m giving at the Second Meeting of the International Society of Phylogenetic Nomenclature, which is being held next week at Yale University. The ISPN is the body associated with PhyloCode, a code being developed for phylogenetic taxonomy (sometimes called “cladistic taxonomy”). My talk is entitled A Mathematical Approach to Defining Clades, Using Order Relations on Sets of Organisms, and hopefully I can make that a bit more interesting than it sounds.

Strips will continue, but I will probably not be writing any new essays until sometime next month.

3 Responses to “ISPN Meeting”
Ezequiel wrote:

hey, for me it sounds great!!!
I found very difficult to implement the cladistic approach in my work (nowadays, fossil Osmundaceae ferns), particularly due the lack of good characters and the great number of species, defined with some old criteria and sometimes without taking into account that living things GROW, so bigger and smaller don´t mean different species… I hope some day I´ll be able to apply the cladistic methodology…

Anyway, man: best wishes and success!!! I´ll be here waiting (as every Tuesday)

Mike Keesey wrote:


My stuff is about nomenclature, not cladistic analysis, though. I’m more concerned with what to do, taxonomically, once you have a phylogenetic hypothesis, not with how to reach that hypothesis.

Milady wrote:

Of course we hear you. Have a look at SINA, I think I wrote it exlctay for what you’re trying to do. If you use the SILVA databases, you can use the online version. If you want to incorporate sequences into your own alignment, you need to download it and run it locally.Say you’ve got new_sequences.fasta and mydatabase.arb. Then running sina -i new_sequences.fasta -o mydatabase.arb ptdb mydatabase.arb overhang=remove will add the aligned and trimmed sequences to your ARB file. Setting overhang=edge will move the bases it can’t match up with your already aligned sequences to the outside of the alignment. Simple enough?Drop me a line if you need help. I love the comic!

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