alignment-integrated reconstruction of ancestral sequences
This repository contains scripts (mostly python and bash) and data/results files associated with the Kolaczkowski Lab's AIRAS project, which calculates ancestral protein sequences while integrating over different alignments.
Further information on the methodology can be found in the project's main peer-reviewed publication:
https://doi.org/10.1093/gbe/evaa164
All data and results files used in the above publication, as well as all scripts and spreadsheets used for data analysis and visualization can be found in the data/ directory. Please see the data/README.md file for more information on data/results files and analysis/visualization scripts available in data/
The main airas.py executable is a Python script that performs alignment-integrated ancestral sequence reconstruction. It has been tested on MAX OS X and should work on any version of UNIX. It requires the following:
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RAxML to perform the ancestral sequence reconstruction. We recommend using RAxML v8 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998144/ https://github.com/stamatak/standard-RAxML You will need to edit line 35 of airas.py to set the RAXML variable to the RAxML v8 executable on your system.
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MAFFT to perform the mapping among all input alignments. We recommend using MAFFT v7 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3603318/ https://mafft.cbrc.jp/alignment/software/ You will need to edit line 36 of airas.py to set the MAFFT variable to the MAFFT v7 executable on your system.
To perform an ancestral sequence reconstruction using airas.py, you first need to generate a binary phylogenetic tree for the sequences you want to analyze. You will also need alignments of your sequences, which you can produce using any sequence-based alignment method (see data/ for the alignment methods used in the AIRAS publication). Once you have a binary tree and multiple different alignments of the same extant sequences, airas.py will integrate ancestral sequence reconstructions at every node on the phylogeny, incorporating information from all sequence alignments.
run ./airas.py -h for usage information.
All information in this repository is provided under the included LICENSE