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Fig. 2 | BMC Bioinformatics

Fig. 2

From: Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life

Fig. 2

a Phylogeny updated with Physcraper using a starting phylogeny and an alignment from [45] (Gottlieb2005 data in text). Tips in original alignment and new tips added with Physcraper are depicted in black and red, respectively. First, Physcraper obtained sequences from the GenBank database via local BLAST of all sequences in the Gottlieb2005 original alignment of the internal transcribed spacer DNA region (ITS). Then, it filtered the obtained sequences following criteria described in section “DNA sequence search and filtering”, and aligned them to the original Gottlieb2005 alignment using MUSCLE. Finally, Physcraper performed a phylogenetic reconstruction using RAxML, with 100 bootstraps. b Results of conflict analysis performed using OpenTree’s conflict tool [44]. The Physcraper updated Gottlieb2005 phylogeny in a was compared to an Ilex OpenTree synthetic subtree v. 12.3 [72] constructed using taxonomy of the genus as backbone and resolving branches based on phylogenetic data from the original Gottlieb2005 phylogeny. Green branches are resolved by the updated phylogeny, blue branches are in agreement between the updated phylogeny and the synthetic subtree, and orange branches are in conflict between the two

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