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:
B.A. Akpınar, Paul O. Carlson, and C.D. Dunn. A novel phylogenetic analysis combined with a machine learning approach predicts human mitochondrial variant pathogenicity. bioRxiv. doi:.
General Information
replace-nonstandard.py – Replaces non-standard nucleotides in a FASTA alignment file with standard nucleotides. The replacement is picked at random, from the IUPAC correspondents that are represented in the alignment for the given position.
Dependency: Bio.SeqIO
Requirement: “IUPAC_nonstandard_codes.txt” file must be in the same folder where the script is run. The use of different code files is possible. Please refer to source code to get more information.
$ python replace-nonstandard.py -a [alignment_file]
extract-correspondence-for-merged-alignment-v.1.1.py - Generates a correspondence file that reports alignment position correspondences of each aligned residue of a species of interest. This correspondence file is later required as input for "AA-presence-lookup-table-v.1.1.py" and "direct-subst-lookup-table-proteins-v.1.1.py" scripts.
Since this script is designed for merged alignments, (1) a list of protein order in the merged alignment file, and (2) a FASTA file of reference sequences for the species of interest are required. The FASTA file of reference sequences does not have to be in the same order as given in the list file, but the names should match. If the alignment file contains only one protein, these two files are still required. Example input and output files are provided in the "Examples" folder.
$ python extract-correspondence-for-merged-alignment-v.1.1.py -a [alignment_file] -r [reference_FASTA_file] -l [list_file]
-conv <species_convention> -o <output_prefix>
Dependency: Bio.SeqIO
AA-presence-lookup-table-v.1.1.py - Generates a look-up table for the presence/absence of the reference amino acid among a list of characters from all or internal tree nodes (including the predicted root) for each position in a given alignment.
Reference amino acid refers to a species of interest, that is specified in the correspondence file, generated by "extract-correspondence-for-merged-alignment-v.1.1.py".
-m flag determines if the search will be within internal or all tree nodes (internal/all; default=all)
$ python AA-presence-lookup-table-v1.1.py -a [alignment_file] -t [tree_file] -corr [correspondence_file] -m <internal/all>
Dependencies: Bio.SeqIO and Bio.Phylo, xlsxwriter
direct-subst-lookup-table-proteins-v.1.1.py - Generates a look-up table for direct substitutions involving the reference amino acid for a given position.
Reference amino acid refers to a species of interest, that is specified in the correspondence file, generated by "extract-correspondence-for-merged-alignment-v.1.1.py".
-m flag determines if the search will be within internal or all tree edges (internal/all; default=all)
$ python direct-subst-lookup-table-proteins-v1.1.py -a [alignment_file] -t [tree_file] -corr [correspondence_file] -m <internal/all>
Dependencies: Bio.SeqIO and Bio.Phylo, xlsxwriter
Usage
Please refer to source codes to get more information. Use --help” or “-h” flags to get usage information.
Contact Bala Ani Akpinar (@aniakpinar) for code-related issues and Cory Dunn (@corydunnlab) for more general inquiries.