Mirarab, Siavash, Nam Nguyen, and Tandy Warnow. “SEPP: SATé-Enabled Phylogenetic Placement.” Pacific Symposium On Biocomputing, 2012, 247–58 (PubMed).
SATé-enabled phylogenetic placement (SEPP) is a software package for phylogenetic placement.
This section details instructions for installing and running version 1.0 of SEPP. This is the version used in the submission of the SEPP paper. Current users should use the latest github version instead of the following instructions. Version 1.0 is provided in this page only to enable replication of the results reported in the paper.
merge.jar
. This jarfile is included in the gzip in the folder location sepp-1.0/sepp/tools/merge.jar
.python <bin>/run_sepp.py -h
"python <bin>/run_sepp.py -t <tree_file> -a <alignment_file> -f <fragment_file> -r <raxml_info_file> -A <alignment_set_size> -P <placement_set_size>
"python <bin>/run_sepp.py -t test.tree -a test.fasta -f test.fas -r test.RAxML_info -A 250 -P 250
python <bin>/run_sepp.py -c sample.config
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