Phylogeny Course Tübingen 2007/2008

Material compiled by M. Göker for the Tübingen 2007 and 2008 phylogeny courses.

Example files

• sequence_formats.zip: Example files for 16 different sequence formats (always same dataset).
• examples.zip: Examples for unaligned molecular datasets.

Documents

• PCMG1.pdf: My manual, the first part (from sequence to alignment).
• Bremer.pdf: Instructions for the computation of Bremer support values.
• Questions.pdf: 2006 phylogeny course questionnaire.
• Supertree.pdf: Instructions for constructing supertrees.

Commented PAUP* batch files

• standard.nex: PAUP* batch file containing my favourite settings. Can be executed before each datafile, but the pset settings are only accepted if a characters or data block is in memory.
• bionj.nex: PAUP* batch file to calculate a BIONJ tree.
• bionj_bootstrap.nex: PAUP* batch file to conduct BIONJ bootstrapping.
• mp_hsearch.nex: PAUP* batch file for heuristic search under the MP criterion. Illustrates the hsearch command options I found most useful and how and why you could change them.
• mp_bootstrap.nex: PAUP* batch file for bootstrapping under the MP criterion.
• tstv.nex: Assumptions block for generalized parsimony that gives transversions twice the cost of transitions.
• mPAM250.nex: Xu & Miranker 2004 metric amino acid matrix as cost matrix for protein parsimony with PAUP*.
• protpars.nex: Metric amino acid matrix to emulate protpars behaviour in PAUP* protein parsimony (not exactly identical, see file!).

Scripts

• See scripts page.

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