Commercial use without the permission of the software authors (Cory Dunn and Bala Ani Akpinar) is forbidden. Academic use is permitted, with citation of the following work:
C.D. Dunn†, B.A. Akpınar, and V. Sharma†. 2019. An unusual amino acid substitution within the hummingbird cytochrome c oxidase alters a key proton-conducting channel. G3: Genes, Genomes, Genetics, 10:7, 2477-2485. doi: 10.1534/g3.120.401312
General Information
binary-table-by-edges-v2.2.py (latest) – Generates a binary table that maps the presence or absence of mutations on the edges of a phylogenetic tree. Dependencies: Bio.SeqIO and Bio.Phylo
binary-table-by-edges-v3.1.py (latest) – Generates a binary table that maps the presence or absence of mutations on the edges of a phylogenetic tree; also adds a species convention if specified. Dependencies: Bio.SeqIO and Bio.Phylo
add-convention-to-binarytable-v1.1.py – Adds a species convention to the binary table generated by binary-table-by-edges-v2.py. Dependency: Bio.SeqIO
extract-position-values_species_and_nodes-v1.1.py – Extracts all possible characters across a tree, for all positions in a given alignment. Dependency: Bio.SeqIO
report-on-F-values-v1.1.py – Depending on the query, which can be a list of edge pairs or a binary table, provides information on fluctuating (mutating) edges in terms of amino acid changes.
Please refer to source code of each package to get more information.
Usage
Use "--help" or "-h" flags to get usage information for each script. All scripts are written in Python 2.7.
Contact Bala Ani Akpinar (@aniakpinar) for code-related issues and Cory Dunn (@corydunnlab) for more general inquiries.