Phylogeny scripts

Scripts designed and implemented by M. Goeker for the Tuebingen 2007/2008 phylogeny courses. The scripts are distributed under the terms of the Gnu Public License V2. If you use any of them in a publication, please cite this web page.

Sequence format conversion

gbk2fas.sed: Convert GenBank flatfile to FASTA format. FASTA sequence labels will consist of organism name and accession number.
gbf2fas.awk: Convert FASTA format downloaded from GenBank into nicer FASTA format. The headers are as above, but the organism name must be guessed; it is not always included in GenBank's FASTA titles!
nex2epf.sed: Convert NEXUS to extended PHYLIP format. Should work with non-interleaved NEXUS exported by PAUP*.

Data cleaning

dufa.awk: Remove duplicate sequences from unaligned FASTA files.

Sequence alignment

dia2nex.sh: Shell wrapper script for the DIALIGN alignment program. The most useful feature is the conversion of DIALIGN's alignment quality scores into characters sets for use PAUP*. I.e., you can find and automatically exclude the least reliably aligned columns. Have a look at the example file. If you use this feature, please cite that paper. Warning: The Macintosh version of Dialign seems to contain a bug. In some sequences, the first character is replaced by the NUL character.
gblocks2nexus.sh: Shell wrapper for Gblocks. Excluded alignment columns are not physically removed from the file, but excluded using the corresponding PAUP* command in the output NEXUS file.
aop.sh: Shell wrapper script for the POA alignment program. Manages POA runs, automatically provides a scoring matrix, cleans FASTA files before and after the run, and computes pair-wise similarity scores with four different methods.
blosum80_ext_tru.mat: Scoring matrix used by aop.sh. It is identical to blosum80_trunc.mat distributed with POA but includes nucleotide ambiguity code.

Working with PAUP*

nexus.pats: NEXUS syntax highlighting for the Nedit editor. Includes all commands, command options, and command option arguments mentioned in the PAUP* 4b10 manual.
bremer.tcl: Script to compute Bremer and partioned Bremer support values in conjunction with PAUP*.

Miscellanea

clean_raxml.sh: Clean up after a RAxML run (get globally best tree and put best trees from each run in a single file).
bash.zip: Bash configuration files. Unpack the archive and put the files in your home directory.