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Supplementary material for 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, Vol. 2, No. 1, pp. 5 - 13; DOI: 10.15698/mic2015.01.182"
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hyp_testing
mrbayes_raw
raxml_100_seeds
raxml_raw
raxml_trimmed_alg
LICENSE
README.md
gname2sp
mrbayes_tree.nw
n-terminus.alg.fa
prx5.alg.fa
prx5.py
raxml_tree.nw
suboptimal_topologies.summary.txt

README.md

Description

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

Notes:

  • All text files use unix new line separator
  • Large intermediate files obtained in some of the analyses are not included
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