This is part of the supplementary material of the paper:
Prokaryotic ancestry of a dual localized peroxiredoxin 5 in malaria parasites. Carine F. Djuika, Jaime Huerta-Cepas, Jude M. Przyborski, Sophia Deil, Cecilia P. Sanchez, Tobias Doerks, Peer Bork, Michael Lanzer, Marcel Deponte. Microbial Cell (2014). In press
The repository contains all the data and scripts used for phylogenetic analyses.
hyp_testing -> Analysis of 96 constraint topologies using CONSEL mrbayes_raw -> Source and configuration files used in MrBayes analysis n-terminus.alg.fa -> Multipl sequence alignment of 3 prx5 sequences, PfAOP including the N-terminus region prx5.alg.fa -> Multiple sequence alignment of the 84 prx5 sequences prx5.py -> Python script for tree analyses raxml_100_seeds -> Raxml test for suboptimal topologies raxml_raw -> Raxml full scan test, with 100 bootstraps (raw files) raxml_tree.nw -> tree from Raxml full scan mrbayes_tree.nw -> tree obtained from Bayesian full scan raxml_trimmed_alg -> Raxml scan using a trimmed version of the alignment suboptimal_topologies.summary.txt -> Condensed summary of all suboptimal topologies found bootstrapped_topologies.summary.txt -> Condensed summary of all bootstrapped topologies found
- All text files use unix new line separator
- Large intermediate files obtained in some of the analyses are not included