#### Description of supplementary materials for Dupuis et al. bioRxiv submission: #### HiMAP: robust Phylogenomics from Highly Multiplexed Amplicon sequencing #### 3 November 2017 ### Dupuis_SuppMat1.zip contains: # Inputs for ASTRAL species tree analysis ASTRAL_INPUT_CONFIG_spp_indsRmvd ASTRAL_INPUT_all_raxml_genetrees.tre # Input configuration file for ExaBayes analysis EXABAYES_INPUT_CONFIG_config.nex # Supplementary Figures S1-S6 Figure_S1-S6.pdf # PartitionFinder input configuration files for the nucleotide ("nt") and peptide ("pep") datasets PARTITIONFINDER_INPUT_CONFIG_partition_finder_nt.cfg PARTITIONFINDER_INPUT_CONFIG_partition_finder_pep.cfg # Input configuration file for PoMo species tree analysis POMO_INPUT_Teph3_878genes_cutInds100_cutGenes200.cf # Input file for SVDquartets species tree analysis SVDQUARTETS_INPUT_Teph3_878genes_cutInds100_cutGenes200_svdq_noLog.nex # Supplementary Tables S1-S5 Tables_S1-S5.xlsx # Filtered, concatenated alignments for main phylogenetic analyses Teph3_878genes_cutInds100_cutGenes200.phy Teph3_878genes_cutInds100_cutGenes200_Peptides.phy ### Additional supplementary materials # Directories containing individual amplicon alignments for nucleotide ("nt") and peptide ("pep") datasets amplicon_alignments_nt.zip amplicon_alignments_pep.zip # Directories containing full input files for HiMAP part01 and part02 (see https://github.com/popphylotools/HiMAP) Full_HiMAP_part01_input.zip Full_HiMAP_part02_input.zip # Directory containing full input files for orthoMCL analysis OrthoMCL_input.zip