Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython

BMC Bioinformatics

Table 2 Performance

Task	Input tree	Python 2.7	Python 3.2	PyPy 1.9
Read a very large Newick tree	Smith 2011 angiosperm supertree
	(55473 terminal nodes) [38]	17.45	16.85	1.214
Read the same large tree in phyloXML	Smith 2011, converted to phyloXML with
	phylo_converter (http://phylosoft.org/)	3.805	4.318	3.937
Write the same large tree as Newick	Smith 2011	0.5238	0.7704	0.4378
Write the same large tree as phyloXML	Smith 2011	10.39	10.85	24.17
Read a medium-sized Newick tree	Davies 2004 angiosperm supertree
	(440 terminal nodes) [39]	0.1097	0.1087	0.007312
Parse many Newick trees	Davies 2004, copies rerooted at
	each node (816 trees)	84.91	84.29	6.812
Reroot at each node	Davies 2004	1.347	1.167	0.3450
Collapse all splits with bootstrap values less than 50	Davies 2004	2.266	2.312	2.411
Total branch length	Davies 2004	0.01322	0.01310	0.01448
Ladderize the tree	Davies 2004	0.1274	0.1190	0.1127
Count terminal nodes	Davies 2004	0.006838	0.006323	0.005914

Performance of Bio.Phylo functions and tree methods under different Python versions on several benchmark tasks. Reported execution times are the median of 101 replications of each task, in seconds (Additional file 2). Benchmarks were evaluated with Python versions 2.7.3 and 3.2.3 and PyPy version 1.9 on an Intel Xeon E5405 2.00 GHz processor with 8 GB memory, running under 64-bit Ubuntu Linux 12.04 with Biopython 1.60 installed.