tree-based orthology inference

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  • License: MIT License (MIT)
  • Author: Felix Thalen
  • Tags orthology inference, orthologs, tree-based, phylogenetics, phylogenomics, orthology
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Project description

What is PhyloPyPruner?

PhyloPyPruner is a Python package for refining the output of a graph-based orthology inference approach such as OrthoMCL, OrthoFinder or HaMStR. Similar to other tree-based orthology inference methods (e.g., PhyloTreePruner, UPhO, Agalma and Phylogenomic Dataset Reconstruction), it uses phylogenetic trees in order to obtain genes that are 1:1 orthologous. In addition to filters and algorithms seen in pre-existing tools, this package provides new methods for differentiating contamination-like sequences from paralogs.

PhyloPyPruner is under active development and I would appreciate it if you try this software on your own data and leave feedback.

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Our manuscript is still in preparation, it will be posted here once a preprint of the article is available.

© Kocot Lab 2018

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  • License: MIT License (MIT)
  • Author: Felix Thalen
  • Tags orthology inference, orthologs, tree-based, phylogenetics, phylogenomics, orthology
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1.2.6

1.2.5

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