LICENSE
MANIFEST.in
README.md
build.sh
setup.py
doc/images/output_example.png
doc/images/paralog_freq.png
doc/images/ppp_logo.png
doc/images/proteomes2orthologs.png
examples/lophotrochozoa/01482.fa
examples/lophotrochozoa/01482.tre
examples/lophotrochozoa/01549.fa
examples/lophotrochozoa/01549.tre
examples/lophotrochozoa/01685.fa
examples/lophotrochozoa/01685.tre
examples/lophotrochozoa/01770.fa
examples/lophotrochozoa/01770.tre
examples/lophotrochozoa/05504.fa
examples/lophotrochozoa/05504.tre
examples/lophotrochozoa/05749.fa
examples/lophotrochozoa/05749.tre
examples/lophotrochozoa/05894.fa
examples/lophotrochozoa/05894.tre
examples/lophotrochozoa/10744.fa
examples/lophotrochozoa/10744.tre
examples/lophotrochozoa/11267.fa
examples/lophotrochozoa/11267.tre
examples/lophotrochozoa/14983.fa
examples/lophotrochozoa/14983.tre
examples/lophotrochozoa/README.txt
examples/lophotrochozoa/abbreviations.csv
examples/lophotrochozoa/subclades.txt
examples/lophotrochozoa/phylopypruner_output/input_alignment_stats.csv
examples/lophotrochozoa/phylopypruner_output/output_alignment_stats.csv
examples/lophotrochozoa/phylopypruner_output/phylopypruner.log
examples/tunicata/0207.fa
examples/tunicata/0207.tre
examples/tunicata/0208.fa
examples/tunicata/0208.tre
examples/tunicata/0228.fa
examples/tunicata/0228.tre
examples/tunicata/0594.fa
examples/tunicata/0594.tre
examples/tunicata/0909.fa
examples/tunicata/0909.tre
examples/tunicata/0946.fa
examples/tunicata/0946.tre
examples/tunicata/0996.fa
examples/tunicata/0996.tre
examples/tunicata/1003.fa
examples/tunicata/1003.tre
examples/tunicata/1025.fa
examples/tunicata/1025.tre
examples/tunicata/1028.fa
examples/tunicata/1028.tre
examples/tunicata/README.txt
examples/tunicata/phylopypruner_output/input_alignment_stats.csv
examples/tunicata/phylopypruner_output/occupancy_matrix.png
examples/tunicata/phylopypruner_output/otu_stats.csv
examples/tunicata/phylopypruner_output/output_alignment_stats.csv
examples/tunicata/phylopypruner_output/paralogy_freq_plot.png
examples/tunicata/phylopypruner_output/partition_data.txt
examples/tunicata/phylopypruner_output/phylopypruner.log
examples/tunicata/phylopypruner_output/supermatrix.fas
examples/tunicata/phylopypruner_output/supermatrix_stats.csv
examples/tunicata/phylopypruner_output/output_alignments/0207_pruned.fa
examples/tunicata/phylopypruner_output/output_alignments/0208_pruned.fa
examples/tunicata/phylopypruner_output/output_alignments/0594_pruned.fa
examples/tunicata/phylopypruner_output/output_alignments/0909_pruned.fa
examples/tunicata/phylopypruner_output/output_alignments/0946_pruned.fa
examples/tunicata/phylopypruner_output/output_alignments/0996_pruned.fa
examples/tunicata/phylopypruner_output/output_alignments/1003_pruned.fa
examples/tunicata/phylopypruner_output/output_alignments/1025_pruned.fa
examples/tunicata/phylopypruner_output/output_alignments/1028_pruned.fa
phylopypruner/VERSION
phylopypruner/__init__.py
phylopypruner/__main__.py
phylopypruner/decontamination.py
phylopypruner/fasta.py
phylopypruner/filtering.py
phylopypruner/gene_partition.py
phylopypruner/log.py
phylopypruner/mask_monophylies.py
phylopypruner/msa.py
phylopypruner/newick.py
phylopypruner/phylopypruner.py
phylopypruner/plot.py
phylopypruner/prune_paralogs.py
phylopypruner/report.py
phylopypruner/root.py
phylopypruner/run.py
phylopypruner/sequence.py
phylopypruner/settings.py
phylopypruner/summary.py
phylopypruner/supermatrix.py
phylopypruner/taxonomic_groups.py
phylopypruner/tree_node.py
phylopypruner/tree_stats.py
phylopypruner.egg-info/PKG-INFO
phylopypruner.egg-info/SOURCES.txt
phylopypruner.egg-info/dependency_links.txt
phylopypruner.egg-info/entry_points.txt
phylopypruner.egg-info/requires.txt
phylopypruner.egg-info/top_level.txt
scripts/phylopypruner