This repository contains supplemental materials from :
Paul Simion, Hervé Philippe, Denis Baurain, Muriel Jager, Daniel J. Richter, Arnaud Di Franco, Béatrice Roure, Nori Satoh, Éric Quéinnec, Alexander Ereskovsky, Pascal Lapébie, Erwan Corre, Frédéric Delsuc, Nicole King, Gert Wörheide, Michaël Manuel, A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals, Current Biology, Available online 16 March 2017, ISSN 0960-9822, http://dx.doi.org/10.1016/j.cub.2017.02.031.
alignements_1719genes.tgz
This archive contains the 1719 alignments as obtained after our complete dataset building protocol.
supermatrix_97sp_401632pos_1719genes.fasta
this file corresponds to the concatenation of the entire dataset (1719 gene alignements).
supermatrix_90sp_136618pos_heterop60.puz
Dataset after the removal of the 60% most heteropecileous sites.
supermatrix_90sp_102464pos_heterop70.puz
Dataset after the removal of the 70% most heteropecileous sites.
supermatrix_90sp_268032pos_dayhoff6.phy
Dayhoff6 recoding of our dataset (constant sites were removed).
You probably want to remove the first line of this file when using other softwares than PhyloBayes.
partition_401632pos_1719genes.part
Partitionning scheme corresponding to the boundaries of the 1719 genes.
supermatrix_whelan2015_81006pos_NoDemo.phy
Dataset from Whelan et al. 2015 in which demosponges have been removed.
supermatrix_whelan2015_81006pos_NoDemoCalcHomo.phy
Dataset from Whelan et al. 2015 in which all sponges except hexactinellides have been removed.
partition_whelan2015_81006pos.part
Partitionning scheme corresponding to the boundaries of the 251 genes from Whelan et al. 2015.
tree_97sp_CAT.tre
10 jackknife replicates of 100,000 position each - CAT+G4 (Phylobayes)
tree_90sp_CAT.tre
100 jackknife replicates of 100,000 position each - CAT+G4 (Phylobayes)
tree_97sp_LGF-PARTITION.tre
100 bootstraps - partitionning by gene - LG+G4+F (RAxML)
tree_90sp_LGF-PARTITION.tre
100 bootstraps - partitionning by gene - LG+G4+F (RAxML)
tree_90sp_CAT_heterop60.tre
2 independant MCMC chains - CAT+G4 (Phylobayes)
tree_90sp_CAT_heterop70.tre
2 independant MCMC chains - CAT+G4 (Phylobayes)
tree_NoDemo_CAT.tre
10 jackknife replicates of 100,000 position each - CAT+G4 (Phylobayes)
tree_NoDemo_LGF-PARTITION.tre
100 bootstraps - partitionning by gene - LG+G4+F (RAxML)
tree_NoDemoCalcHomo_CAT.tre
10 jackknife replicates of 100,000 position each - CAT+G4 (Phylobayes)
tree_NoDemoCalcHomo_LGF-PARTITION.tre
100 bootstraps - partitionning by gene - LG+G4+F (RAxML)
tree_Whelan2015_NoDemo_CAT.tre
2 independant MCMC chains - CAT+G4 (Phylobayes)
tree_Whelan2015_NoDemo_LGF-PARTITION.tre
100 bootstraps - partitionning by gene - LG+G4+F (RAxML)
tree_Whelan2015_NoDemoCalcHomo_CAT.tre
2 independant MCMC chains - CAT+G4 (Phylobayes)
tree_Whelan2015_NoDemoCalcHomo_LGF-PARTITION.tre
100 bootstraps - partitionning by gene - LG+G4+F (RAxML)
tree_rpl2_FIFO.pdf
rpl2 tree when using initial datasets (right after the Filter Focus step - FIFO).
tree_rpl2_DCC.pdf
rpl2 tree when using datasets after the De-Cross-Contamination step (DCC).
tree_rpl2_DC1.pdf
rpl2 tree when using datasets after the De-Contamination step 1 (DC1).
tree_rpl2_DC2.pdf
rpl2 tree when using datasets after the De-Contamination step 2 (DC2).
tree_rpl2_DC3.pdf
rpl2 tree when using datasets after the De-Contamination step 3 (DC3).
tree_rpl2_FINAL.pdf
Final rpl2 tree after all cleaning steps of our pipeline, as used for supermatrix concatenation.
utilities_src.tgz
These are the sources of the C programs used in our dataset assembly procedure.
Please note that the "De-Cross-Contamination" (DCC) step of our procedure has been re-worked
as a dedicated software (named "CroCo") currently under final development and that will be published elsewhere.
taxon_names.dict
This dictionnary indicates the corresponds between full taxon names and their short version found in phylip files.
choanoflagellate names
Choanoflagellate names used in our study corresponds to the valid names recently published by Carr et al. (2016).
The Post-Publication_Materials_following_arising_questions folder contains additional files and analyses details that we made available following arising technical questions.
Post-publication_Note.pdf
Additional note on the MCMC convergence approximation strategy used and on the further evaluation of chain convergence.
100_jackknife_replicates_90sp_CAT.trees
All jackknife trees corresponding to the 100 replicates used to build tree_90sp_CAT.tre - CAT+G4 (Phylobayes)
10_jackknife_replicates_97sp_CAT.trees
All jackknife trees corresponding to the 10 replicates used to build tree_97sp_CAT.tre - CAT+G4 (Phylobayes)
10_jackknife_replicates_80sp_CAT.trees
All jackknife trees corresponding to the 10 replicates used to build tree_NoDemo_CAT.tre - CAT+G4 (Phylobayes)
10_jackknife_replicates_70sp_CAT.trees
All jackknife trees corresponding to the 10 replicates used to build tree_NoDemoCalcHomo_CAT.tre - CAT+G4 (Phylobayes)